Problem with installing GBrowse

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Problem with installing GBrowse

Hufeng Zhou
Hello:
I have some problem with GBrowse, during the installation it has some errors so higher versions won't be able to install, I was only able to install GBrowse-1.66.

I can access http://localhost/gbrowse/ without any problems, and all the html pages can be viewed, the problem is in the welcome page, it suggest me to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data. But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be accessed, which shows not found error.

I am wondering if it is GBrowse is not running? If there is any way to resolve this issue? Thanks very much.

After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

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Re: Problem with installing GBrowse

Scott Cain
I forgot to cc the GBrowse mailing list; Hufeng, please reply to this email so it stays on list.

Scott


On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Sorry it took so long to get to this message; it was caught in the spam trap that doesn't allow non-members to post to the list.

Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66 is extremely old.  What were the problems you had?

If you really want to continue with 1.66, please look in the apache access log to see where apache is looking for the gbrowse cgi script, and then try to find where it did get installed.  Since distros are different with regard to where they put various files, it can be difficult for me to guess where they are.  One possible suggestion that sometimes trips up new users is this: if you tried to install GBrowse before you installed apache, the GBrowse installer may have created a /usr/local/apache directory for you.  If it did, I suggest you remove that directory and reinstall GBrowse.

Scott


On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <[hidden email]> wrote:
Hello:
I have some problem with GBrowse, during the installation it has some errors so higher versions won't be able to install, I was only able to install GBrowse-1.66.

I can access http://localhost/gbrowse/ without any problems, and all the html pages can be viewed, the problem is in the welcome page, it suggest me to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data. But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be accessed, which shows not found error.

I am wondering if it is GBrowse is not running? If there is any way to resolve this issue? Thanks very much.

After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Scott Cain
In reply to this post by Hufeng Zhou
Hi Hufeng,

Please keep this on the GBrowse mailing list (reply-all).

I don't understand why you haven't tried to update the version of Bio::Graphics first, since the GBrowse installer asked you to install it.

Can you point me to the documentation for ChiA-PET, because I have heard of people using ChiA-PET data with GBrowse2.

Scott


On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much for your reply.

It is like this, I need to use a package called the ChiA-PET tool that
need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)

So I am trying to install the GBrowse version 1....

If I try to install Version 1.7

I will have following error

Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You probably need to update your BioPerl to version 1.6 or better and
install Bio::Graphics separately from CPAN.

Died at Makefile.PL line 272, <DATA> line 192.


That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even run
the example data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).

I really need your help on this.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> Sorry it took so long to get to this message; it was caught in the spam trap
> that doesn't allow non-members to post to the list.
>
> Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66 is
> extremely old.  What were the problems you had?
>
> If you really want to continue with 1.66, please look in the apache access
> log to see where apache is looking for the gbrowse cgi script, and then try
> to find where it did get installed.  Since distros are different with regard
> to where they put various files, it can be difficult for me to guess where
> they are.  One possible suggestion that sometimes trips up new users is
> this: if you tried to install GBrowse before you installed apache, the
> GBrowse installer may have created a /usr/local/apache directory for you.
> If it did, I suggest you remove that directory and reinstall GBrowse.
>
> Scott
>
>
> On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Hello:
>> I have some problem with GBrowse, during the installation it has some
>> errors so higher versions won't be able to install, I was only able to
>> install GBrowse-1.66.
>>
>> I can access http://localhost/gbrowse/ without any problems, and all the
>> html pages can be viewed, the problem is in the welcome page, it suggest me
>> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data.
>> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> accessed, which shows not found error.
>>
>> I am wondering if it is GBrowse is not running? If there is any way to
>> resolve this issue? Thanks very much.
>>
>> After installation,
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Thanks very much for your help.
I use this version of bioperl because,

Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
from source code this way:

 git clone https://github.com/bioperl/bioperl-live.git
 cd bioperl-live
 perl Build.PL
 ./Build test
 sudo ./Build install


http://gmod.org/wiki/GBrowse_2.0_Prerequisites

And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in installing
the latest version of bioperl but I forced to install the latest
version some how.

You can get the manual of ChiA-pet tool here.

http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:

> Hi Hufeng,
>
> Please keep this on the GBrowse mailing list (reply-all).
>
> I don't understand why you haven't tried to update the version of
> Bio::Graphics first, since the GBrowse installer asked you to install it.
>
> Can you point me to the documentation for ChiA-PET, because I have heard of
> people using ChiA-PET data with GBrowse2.
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Dear Scott:
>>
>> Thanks very much for your reply.
>>
>> It is like this, I need to use a package called the ChiA-PET tool that
>> need to only use GBrowse version 1 (they mentioned on their manual,
>> version 2 won't work)
>>
>> So I am trying to install the GBrowse version 1....
>>
>> If I try to install Version 1.7
>>
>> I will have following error
>>
>> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> You probably need to update your BioPerl to version 1.6 or better and
>> install Bio::Graphics separately from CPAN.
>>
>> Died at Makefile.PL line 272, <DATA> line 192.
>>
>>
>> That is why I tried version. 1.66 it is the only package I can
>> install, but after I install it, I find version 1.66 can not even run
>> the example data.
>> An example in-memory database from yeast chromosome 1 has been
>> installed for you. Try it at this URL:
>> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>>
>> I really need your help on this.
>>
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  +1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Sorry it took so long to get to this message; it was caught in the spam
>> > trap
>> > that doesn't allow non-members to post to the list.
>> >
>> > Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66
>> > is
>> > extremely old.  What were the problems you had?
>> >
>> > If you really want to continue with 1.66, please look in the apache
>> > access
>> > log to see where apache is looking for the gbrowse cgi script, and then
>> > try
>> > to find where it did get installed.  Since distros are different with
>> > regard
>> > to where they put various files, it can be difficult for me to guess
>> > where
>> > they are.  One possible suggestion that sometimes trips up new users is
>> > this: if you tried to install GBrowse before you installed apache, the
>> > GBrowse installer may have created a /usr/local/apache directory for
>> > you.
>> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Hello:
>> >> I have some problem with GBrowse, during the installation it has some
>> >> errors so higher versions won't be able to install, I was only able to
>> >> install GBrowse-1.66.
>> >>
>> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> the
>> >> html pages can be viewed, the problem is in the welcome page, it
>> >> suggest me
>> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> data.
>> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> accessed, which shows not found error.
>> >>
>> >> I am wondering if it is GBrowse is not running? If there is any way to
>> >> resolve this issue? Thanks very much.
>> >>
>> >> After installation,
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  +1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >>
>> >> _______________________________________________
>> >> Gmod-gbrowse mailing list
>> >> [hidden email]
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Scott Cain
Hi Hufeng,

BioPerl and BioGraphics are two different things.  I suspect BioPerl from git will work fine, you must also install BioGraphics, most easily done with CPAN:

cpan
cpan> install Bio::Graphics

Which will get you the most recent release of BioGraphics.  Then you should be able to install GBrowse 1.70, which is the most recent version of GBrowse 1 available (though that's still 5 years old). 

I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a GBrowse configuration file for you, which I suppose is some benefit as you can't directly use a GBrowse 1 configuration file with GBrowse2.  The data that it generates is (I believe) compatible with GBrowse2 as well as JBrowse (which is *much* easier to set up).

Scott


On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]> wrote:
Thanks very much for your help.
I use this version of bioperl because,

Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
from source code this way:

 git clone https://github.com/bioperl/bioperl-live.git
 cd bioperl-live
 perl Build.PL
 ./Build test
 sudo ./Build install


http://gmod.org/wiki/GBrowse_2.0_Prerequisites

And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in installing
the latest version of bioperl but I forced to install the latest
version some how.

You can get the manual of ChiA-pet tool here.

http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> Please keep this on the GBrowse mailing list (reply-all).
>
> I don't understand why you haven't tried to update the version of
> Bio::Graphics first, since the GBrowse installer asked you to install it.
>
> Can you point me to the documentation for ChiA-PET, because I have heard of
> people using ChiA-PET data with GBrowse2.
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Dear Scott:
>>
>> Thanks very much for your reply.
>>
>> It is like this, I need to use a package called the ChiA-PET tool that
>> need to only use GBrowse version 1 (they mentioned on their manual,
>> version 2 won't work)
>>
>> So I am trying to install the GBrowse version 1....
>>
>> If I try to install Version 1.7
>>
>> I will have following error
>>
>> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> You probably need to update your BioPerl to version 1.6 or better and
>> install Bio::Graphics separately from CPAN.
>>
>> Died at Makefile.PL line 272, <DATA> line 192.
>>
>>
>> That is why I tried version. 1.66 it is the only package I can
>> install, but after I install it, I find version 1.66 can not even run
>> the example data.
>> An example in-memory database from yeast chromosome 1 has been
>> installed for you. Try it at this URL:
>> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>>
>> I really need your help on this.
>>
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Sorry it took so long to get to this message; it was caught in the spam
>> > trap
>> > that doesn't allow non-members to post to the list.
>> >
>> > Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66
>> > is
>> > extremely old.  What were the problems you had?
>> >
>> > If you really want to continue with 1.66, please look in the apache
>> > access
>> > log to see where apache is looking for the gbrowse cgi script, and then
>> > try
>> > to find where it did get installed.  Since distros are different with
>> > regard
>> > to where they put various files, it can be difficult for me to guess
>> > where
>> > they are.  One possible suggestion that sometimes trips up new users is
>> > this: if you tried to install GBrowse before you installed apache, the
>> > GBrowse installer may have created a /usr/local/apache directory for
>> > you.
>> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Hello:
>> >> I have some problem with GBrowse, during the installation it has some
>> >> errors so higher versions won't be able to install, I was only able to
>> >> install GBrowse-1.66.
>> >>
>> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> the
>> >> html pages can be viewed, the problem is in the welcome page, it
>> >> suggest me
>> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> data.
>> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> accessed, which shows not found error.
>> >>
>> >> I am wondering if it is GBrowse is not running? If there is any way to
>> >> resolve this issue? Thanks very much.
>> >>
>> >> After installation,
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >>
>> >> _______________________________________________
>> >> Gmod-gbrowse mailing list
>> >> [hidden email]
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:

> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  +1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  +1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  +1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research


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Re: Problem with installing GBrowse

Scott Cain
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Problem with installing GBrowse

Scott Cain
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Really large sessions necessary?

Ryan Doherty-2
In reply to this post by Scott Cain
Hi, a while ago we transitioned from using file-based CGI sessions (and
disallowing user login) to allowing login and storing user sessions in
an Oracle database.  Since the sessions are read (and written?) with
every request, the size of the session data is a concern for us.  We've
had some problems with row locking and DB blocks when executing "update
table sessions set a_session=:p1 where id=:p2", and while the session
size may or may not be a problem, we'd like to minimize the cost and
frequency of these updates.

I've attached one of our larger persistent user sessions.  We do have a
large number of tracks in some instances, but it looks like the session
records both tracks that are turned on and those turned off, and also
contains multiple session snapshots.  I just wonder if this is by
design, or can be configured away?  Maybe someone could explain what all
data is contained in the user session and why they grow so big?  And is
there a way to reduce write contention between requests from the same
client/browser?

Thanks,
Ryan Doherty
EuPathDB Team

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Really large sessions necessary?

Ryan Doherty-2
Hi, a while ago we transitioned from using file-based CGI sessions (and
disallowing user login) to allowing login and storing user sessions in
an Oracle database. Since the sessions are read (and written?) with
every request, the size of the session data is a concern for us. We've
had some problems with row locking and DB blocks when executing "update
table sessions set a_session=:p1 where id=:p2", and while the session
size may or may not be a problem, we'd like to minimize the cost and
frequency of these updates.

I've attached one of our larger persistent user sessions. We do have a
large number of tracks in some instances, but it looks like the session
records both tracks that are turned on and those turned off, and also
contains multiple session snapshots. I just wonder if this is by design,
or can be configured away? Maybe someone could explain what all data is
contained in the user session and why they grow so big? And is there a
way to reduce write contention between requests from the same
client/browser?

Thanks,
Ryan Doherty
EuPathDB Team


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Re: Problem with installing GBrowse

Hufeng Zhou
In reply to this post by Hufeng Zhou
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Problem with installing GBrowse

Scott Cain
Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it? 


On Thu, Nov 13, 2014 at 12:48 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.

hufeng@kiefflab-cloud:~/Programs/ChIA-PET-tool/pipeline$ ls -l /usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root  35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root   9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root  15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root   4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root  35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root  49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root  51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root    905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root   4166 Sep  1 17:00 tutorial_test.pl


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 4:51 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it? 


On Thu, Nov 13, 2014 at 12:48 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Problem with installing GBrowse

Scott Cain
Hi Hufeng,

The only other thing I can think of is that apache isn't configured to process cgi scripts yet. That used to be on by default in most configurations, but that's becoming less common.  Try this:

  sudo a2enmod cgi

To turn it on. 

Scott

Sent from my iPad

On Nov 13, 2014, at 4:54 PM, Hufeng Zhou <[hidden email]> wrote:

Dear Scott:
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.

hufeng@kiefflab-cloud:~/Programs/ChIA-PET-tool/pipeline$ ls -l /usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root  35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root   9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root  15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root   4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root  35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root  49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root  51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root    905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root   4166 Sep  1 17:00 tutorial_test.pl


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 4:51 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it? 


On Thu, Nov 13, 2014 at 12:48 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:
Thanks very much, yeah, it is not enabled previous,

so I enable that according to your suggestions as follows.

hufeng@kiefflab-cloud:~$ sudo a2enmod cgi
[sudo] password for hufeng:
Enabling module cgi.
To activate the new configuration, you need to run:
  service apache2 restart
hufeng@kiefflab-cloud:~$ service apache2 restart
 * Restarting web server apache2                                                                                                                                                                        [fail]
hufeng@kiefflab-cloud:~$ sudo a2enmod cgi
Module cgi already enabled
hufeng@kiefflab-cloud:~$


It is already enabled.
But
http://localhost/cgi-bin/gbrowse/yeast
nor
http://localhost/cgi-bin/gbrowse/
nor
http://localhost/cgi-bin

can be accessed on the browser.

Sorry for so many problems,
If it is possible you can also access to my server through teamview, (ssh access won't be possible. since the network is protected by the firewall.)


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 8:37 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

The only other thing I can think of is that apache isn't configured to process cgi scripts yet. That used to be on by default in most configurations, but that's becoming less common.  Try this:

  sudo a2enmod cgi

To turn it on. 

Scott

Sent from my iPad

On Nov 13, 2014, at 4:54 PM, Hufeng Zhou <[hidden email]> wrote:

Dear Scott:
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.

hufeng@kiefflab-cloud:~/Programs/ChIA-PET-tool/pipeline$ ls -l /usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root  35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root   9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root  15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root   4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root  35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root  49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root  51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root    905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root   4166 Sep  1 17:00 tutorial_test.pl


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 4:51 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it? 


On Thu, Nov 13, 2014 at 12:48 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth discussion and help, I am very grateful.

I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.

Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10.  I will try to install Apache1. at the moment.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 3:11 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)?  The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.  

I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software.  Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse.  One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2.  The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer).  If I knew what distro you were using, I could probably suggest the correct values for those items.

Scott


On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much for your willingness to help.

it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Here localhost/ is the directory on my server,/var/www/

hufeng@kiefflab-cloud:~/Programs$ ls -l /var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep  1 17:00 gbrowse
drwxr-xr-x  4 root root 4096 Oct 24 17:05 html

but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin

I am wondering if that is the causes of the issue?

So I need your help on this issue, thanks very much.


Here pasted the detail history of how I install the GBrowse1.70,
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache2/conf
       HTDOCS /usr/local/apache2/htdocs
       CGIBIN /usr/local/apache2/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.95 cusr  0.03 csys =  1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.

But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1

Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Wed, Nov 12, 2014 at 8:29 AM, Scott Cain <[hidden email]> wrote:
> Hi Hufeng,
>
> BioPerl and BioGraphics are two different things.  I suspect BioPerl from
> git will work fine, you must also install BioGraphics, most easily done with
> CPAN:
>
> cpan
> cpan> install Bio::Graphics
>
> Which will get you the most recent release of BioGraphics.  Then you should
> be able to install GBrowse 1.70, which is the most recent version of GBrowse
> 1 available (though that's still 5 years old).
>
> I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
> GBrowse configuration file for you, which I suppose is some benefit as you
> can't directly use a GBrowse 1 configuration file with GBrowse2.  The data
> that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
> (which is *much* easier to set up).
>
> Scott
>
>
> On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <[hidden email]>
> wrote:
>>
>> Thanks very much for your help.
>> I use this version of bioperl because,
>>
>> Packaged versions of BioPerl contain a bug that prevents GBrowse from
>> displaying DNA sequences from in-memory databases. Install Bioperl
>> from source code this way:
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>>  cd bioperl-live
>>  perl Build.PL
>>  ./Build test
>>  sudo ./Build install
>>
>>
>> http://gmod.org/wiki/GBrowse_2.0_Prerequisites
>>
>> And I find most of the bioperl version are quite old, may I know what
>> is the recommended version? I actually have some problem in installing
>> the latest version of bioperl but I forced to install the latest
>> version some how.
>>
>> You can get the manual of ChiA-pet tool here.
>>
>> http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
>>
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Hufeng,
>> >
>> > Please keep this on the GBrowse mailing list (reply-all).
>> >
>> > I don't understand why you haven't tried to update the version of
>> > Bio::Graphics first, since the GBrowse installer asked you to install
>> > it.
>> >
>> > Can you point me to the documentation for ChiA-PET, because I have heard
>> > of
>> > people using ChiA-PET data with GBrowse2.
>> >
>> > Scott
>> >
>> >
>> > On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Scott:
>> >>
>> >> Thanks very much for your reply.
>> >>
>> >> It is like this, I need to use a package called the ChiA-PET tool that
>> >> need to only use GBrowse version 1 (they mentioned on their manual,
>> >> version 2 won't work)
>> >>
>> >> So I am trying to install the GBrowse version 1....
>> >>
>> >> If I try to install Version 1.7
>> >>
>> >> I will have following error
>> >>
>> >> Installed Bio::Graphics version 1.654 is less than desired version 1.7.
>> >> You probably need to update your BioPerl to version 1.6 or better and
>> >> install Bio::Graphics separately from CPAN.
>> >>
>> >> Died at Makefile.PL line 272, <DATA> line 192.
>> >>
>> >>
>> >> That is why I tried version. 1.66 it is the only package I can
>> >> install, but after I install it, I find version 1.66 can not even run
>> >> the example data.
>> >> An example in-memory database from yeast chromosome 1 has been
>> >> installed for you. Try it at this URL:
>> >> http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
>> >>
>> >> I really need your help on this.
>> >>
>> >>
>> >> Best Regards,
>> >> Hufeng Zhou, Ph. D
>> >> Research Fellow at Brigham and Women's Hospital
>> >> Postdoc Research Fellow at Harvard Medical School
>> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >>
>> >>
>> >> On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Hufeng,
>> >> >
>> >> > Sorry it took so long to get to this message; it was caught in the
>> >> > spam
>> >> > trap
>> >> > that doesn't allow non-members to post to the list.
>> >> >
>> >> > Is there a reason you aren't trying to install GBrowse2?  GBrowse
>> >> > 1.66
>> >> > is
>> >> > extremely old.  What were the problems you had?
>> >> >
>> >> > If you really want to continue with 1.66, please look in the apache
>> >> > access
>> >> > log to see where apache is looking for the gbrowse cgi script, and
>> >> > then
>> >> > try
>> >> > to find where it did get installed.  Since distros are different with
>> >> > regard
>> >> > to where they put various files, it can be difficult for me to guess
>> >> > where
>> >> > they are.  One possible suggestion that sometimes trips up new users
>> >> > is
>> >> > this: if you tried to install GBrowse before you installed apache,
>> >> > the
>> >> > GBrowse installer may have created a /usr/local/apache directory for
>> >> > you.
>> >> > If it did, I suggest you remove that directory and reinstall GBrowse.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hello:
>> >> >> I have some problem with GBrowse, during the installation it has
>> >> >> some
>> >> >> errors so higher versions won't be able to install, I was only able
>> >> >> to
>> >> >> install GBrowse-1.66.
>> >> >>
>> >> >> I can access http://localhost/gbrowse/ without any problems, and all
>> >> >> the
>> >> >> html pages can be viewed, the problem is in the welcome page, it
>> >> >> suggest me
>> >> >> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
>> >> >> data.
>> >> >> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> >> >> accessed, which shows not found error.
>> >> >>
>> >> >> I am wondering if it is GBrowse is not running? If there is any way
>> >> >> to
>> >> >> resolve this issue? Thanks very much.
>> >> >>
>> >> >> After installation,
>> >> >> Best Regards,
>> >> >> Hufeng Zhou, Ph. D
>> >> >> Research Fellow at Brigham and Women's Hospital
>> >> >> Postdoc Research Fellow at Harvard Medical School
>> >> >> Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
>> >> >> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-gbrowse mailing list
>> >> >> [hidden email]
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Problem with installing GBrowse

Hufeng Zhou
Dear Scott:
I reinstall the GBrowse 1.7 but the problem still persists, do you think if I reinstall apache2 would be better? or install apach1?

Here is the log of re-installation.

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
[sudo] password for hufeng:

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.01 sys +  0.98 cusr  0.02 csys =  1.04 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Can't create cgi-bin/gbrowse: Permission denied at cgi-bin/gbrowse.PLS line 26.
make: *** [cgi-bin/gbrowse] Error 13
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Fri, Nov 14, 2014 at 9:53 AM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:
Thanks very much, yeah, it is not enabled previous,

so I enable that according to your suggestions as follows.

hufeng@kiefflab-cloud:~$ sudo a2enmod cgi
[sudo] password for hufeng:
Enabling module cgi.
To activate the new configuration, you need to run:
  service apache2 restart
hufeng@kiefflab-cloud:~$ service apache2 restart
 * Restarting web server apache2                                                                                                                                                                        [fail]
hufeng@kiefflab-cloud:~$ sudo a2enmod cgi
Module cgi already enabled
hufeng@kiefflab-cloud:~$


It is already enabled.
But
http://localhost/cgi-bin/gbrowse/yeast
nor
http://localhost/cgi-bin/gbrowse/
nor
http://localhost/cgi-bin

can be accessed on the browser.

Sorry for so many problems,
If it is possible you can also access to my server through teamview, (ssh access won't be possible. since the network is protected by the firewall.)


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 8:37 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

The only other thing I can think of is that apache isn't configured to process cgi scripts yet. That used to be on by default in most configurations, but that's becoming less common.  Try this:

  sudo a2enmod cgi

To turn it on. 

Scott

Sent from my iPad

On Nov 13, 2014, at 4:54 PM, Hufeng Zhou <[hidden email]> wrote:

Dear Scott:
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.

hufeng@kiefflab-cloud:~/Programs/ChIA-PET-tool/pipeline$ ls -l /usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root  35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root   9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root  15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root   4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root  35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root  49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root  51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root    905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root   4166 Sep  1 17:00 tutorial_test.pl


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 4:51 PM, Scott Cain <[hidden email]> wrote:
Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it? 


On Thu, Nov 13, 2014 at 12:48 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.

So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/

And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,

I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast

which always shows

The requested URL /cgi-bin/gbrowse/yeast was not found on this server.


Apache/2.4.7 (Ubuntu) Server at localhost Port 80


hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL

Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)? 
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /etc/apache2
       HTDOCS /var/www/html
       CGIBIN /usr/lib/cgi-bin
 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  1 wallclock secs ( 0.03 usr  0.00 sys +  0.91 cusr  0.08 csys =  1.02 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################




Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:31 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thanks very much, I deleted the /usr/local/apache2


but the problem persist, I still can not access the exemplary data here.

http://localhost/cgi-bin/gbrowse/yeast_chr1

hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
                File Paths

         CONF /usr/local/apache/conf
       HTDOCS /usr/local/apache/htdocs
       CGIBIN /usr/local/apache/cgi-bin

 GBROWSE_ROOT gbrowse
 INSTALL_BASE
          LIB
          BIN
          YES
       PREFIX
  PACKAGE_DIR
        DO_XS 1
      NONROOT
      SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp  -typemap /usr/share/perl/5.18/ExtUtils/typemap  CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE"   CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc  -shared -L/usr/local/lib -fstack-protector CAlign.o  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so     \
             \
     
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok  
t/02.wiggle.t ...... ok    
t/GBrowse_Chado.t .. ok    
All tests successful.
Files=3, Tests=61,  2 wallclock secs ( 0.03 usr  0.00 sys +  0.98 cusr  0.07 csys =  1.08 CPU)

Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
hufeng@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
hufeng@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1" 
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  <a href="tel:%2B1-%28617%29-903-8599" value="+16179038599" target="_blank">+1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

On Thu, Nov 13, 2014 at 12:20 PM, Scott Cain <[hidden email]> wrote:
No--you want apache2.  If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.



On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <[hidden email]> wrote:
Dear Scott:

Thank you very much indeed for the indepth dis