Gbrowse installation on CentOS

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Gbrowse installation on CentOS

Omar Darwish
Hello all,

What i the easiest way to install Gbrowse2 on CentOS & Fedora ??

--
Thank you,


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Re: Gbrowse installation on CentOS

Scott Cain



Hi Omar,

>From source/the cpan shell since there aren't RPMs for GBrowse (though
there is a debian package that works with debian and ubuntu).  Also,
if you can turn off SELinux it makes life easier.

Scott

On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]> wrote:

> Hello all,
>
> What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>
> --
> Thank you,
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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



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Re: Gbrowse installation on CentOS

Scott Cain
cc'ing to the gbrowse mailing list.

On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]> wrote:

> Hi Omar,
>
> From source/the cpan shell since there aren't RPMs for GBrowse (though
> there is a debian package that works with debian and ubuntu).  Also,
> if you can turn off SELinux it makes life easier.
>
> Scott
>
> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]> wrote:
>> Hello all,
>>
>> What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>>
>> --
>> Thank you,
>>
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> 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: Gbrowse installation on CentOS

Omar Darwish
In reply to this post by Scott Cain
Thanks Scott, I'll give it a try and get back to you



On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

>From source/the cpan shell since there aren't RPMs for GBrowse (though
there is a debian package that works with debian and ubuntu).  Also,
if you can turn off SELinux it makes life easier.

Scott

On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]> wrote:
> Hello all,
>
> What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>
> --
> Thank you,
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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



--
Regards,
Omar

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Re: Gbrowse installation on CentOS

Omar Darwish
Hi Scott,
I tried this command,
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked on Ubuntu but returned errors on both Fedora & CentOS.
What do you think?

Thanks,

On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]> wrote:
Thanks Scott, I'll give it a try and get back to you



On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

>From source/the cpan shell since there aren't RPMs for GBrowse (though
there is a debian package that works with debian and ubuntu).  Also,
if you can turn off SELinux it makes life easier.

Scott

On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]> wrote:
> Hello all,
>
> What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>
> --
> Thank you,
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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



--
Regards,
Omar



--
Regards,
Omar

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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

What sort of errors?  Do you have developers tools like make and gcc installed?

Scott

PS: I took the gmane list out of the cc list and added GBrowse.

On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]> wrote:

> Hi Scott,
> I tried this command,
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
> on Ubuntu but returned errors on both Fedora & CentOS.
> What do you think?
>
> Thanks,
>
>
> On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]> wrote:
>>
>> Thanks Scott, I'll give it a try and get back to you
>>
>>
>>
>> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Omar,
>>>
>>> From source/the cpan shell since there aren't RPMs for GBrowse (though
>>> there is a debian package that works with debian and ubuntu).  Also,
>>> if you can turn off SELinux it makes life easier.
>>>
>>> Scott
>>>
>>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]>
>>> wrote:
>>> > Hello all,
>>> >
>>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>>> >
>>> > --
>>> > Thank you,
>>> >
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > This SF email is sponsosred by:
>>> > Try Windows Azure free for 90 days Click Here
>>> > http://p.sf.net/sfu/sfd2d-msazure
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>>
>> --
>> Regards,
>> Omar
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Omar Darwish
Below the last lines i got from the Installation process, I am not sure if they can help:

Test Summary Report
-------------------
t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
  Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
                36, 40, 42, 47, 76
  Non-zero exit status: 17
t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 90 tests but ran 0.
t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 47 tests but ran 0.
t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 26 tests but ran 0.
t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 3 tests but ran 0.
Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97 cusr  0.25 csys =  2.28 CPU)
Result: FAIL
Failed 7/9 test programs. 17/90 subtests failed.
  LDS/GBrowse-2.48.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/GBrowse-2.48.tar.gz
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build install
  make test had returned bad status, won't install without force







On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

What sort of errors?  Do you have developers tools like make and gcc installed?

Scott

PS: I took the gmane list out of the cc list and added GBrowse.

On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]> wrote:
> Hi Scott,
> I tried this command,
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
> on Ubuntu but returned errors on both Fedora & CentOS.
> What do you think?
>
> Thanks,
>
>
> On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]> wrote:
>>
>> Thanks Scott, I'll give it a try and get back to you
>>
>>
>>
>> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Omar,
>>>
>>> From source/the cpan shell since there aren't RPMs for GBrowse (though
>>> there is a debian package that works with debian and ubuntu).  Also,
>>> if you can turn off SELinux it makes life easier.
>>>
>>> Scott
>>>
>>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]>
>>> wrote:
>>> > Hello all,
>>> >
>>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>>> >
>>> > --
>>> > Thank you,
>>> >
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > This SF email is sponsosred by:
>>> > Try Windows Azure free for 90 days Click Here
>>> > http://p.sf.net/sfu/sfd2d-msazure
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>>
>> --
>> Regards,
>> Omar
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

That is a pretty massive failure--it looks like all of the tests
failed to even run.  Did the prerequisites installed with the cpan
shell install properly?

Scott


On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]> wrote:

> Below the last lines i got from the Installation process, I am not sure if
> they can help:
>
> Test Summary Report
> -------------------
> t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>                 36, 40, 42, 47, 76
>   Non-zero exit status: 17
> t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
> t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: No plan found in TAP output
> t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 47 tests but ran 0.
> t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: No plan found in TAP output
> t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
> t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
> Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97 cusr  0.25
> csys =  2.28 CPU)
> Result: FAIL
> Failed 7/9 test programs. 17/90 subtests failed.
>   LDS/GBrowse-2.48.tar.gz
>   ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>   reports LDS/GBrowse-2.48.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store persistent
> state
> Running Build install
>   make test had returned bad status, won't install without force
>
>
>
>
>
>
>
> On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> What sort of errors?  Do you have developers tools like make and gcc
>> installed?
>>
>> Scott
>>
>> PS: I took the gmane list out of the cc list and added GBrowse.
>>
>> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> > I tried this command,
>> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
>> > on Ubuntu but returned errors on both Fedora & CentOS.
>> > What do you think?
>> >
>> > Thanks,
>> >
>> >
>> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]>
>> > wrote:
>> >>
>> >> Thanks Scott, I'll give it a try and get back to you
>> >>
>> >>
>> >>
>> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Hi Omar,
>> >>>
>> >>> From source/the cpan shell since there aren't RPMs for GBrowse (though
>> >>> there is a debian package that works with debian and ubuntu).  Also,
>> >>> if you can turn off SELinux it makes life easier.
>> >>>
>> >>> Scott
>> >>>
>> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]>
>> >>> wrote:
>> >>> > Hello all,
>> >>> >
>> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>> >>> >
>> >>> > --
>> >>> > Thank you,
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> > ------------------------------------------------------------------------------
>> >>> > This SF email is sponsosred by:
>> >>> > Try Windows Azure free for 90 days Click Here
>> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >>> > _______________________________________________
>> >>> > 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
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Regards,
>> >> Omar
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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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http://p.sf.net/sfu/sfd2d-msazure
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Re: Gbrowse installation on CentOS

Omar Darwish
Oh, I am not really sure about your question, Is there any way (command) i can save the installation output to a file so that i can send it to you ?

Thanks

On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

That is a pretty massive failure--it looks like all of the tests
failed to even run.  Did the prerequisites installed with the cpan
shell install properly?

Scott


On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]> wrote:
> Below the last lines i got from the Installation process, I am not sure if
> they can help:
>
> Test Summary Report
> -------------------
> t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>                 36, 40, 42, 47, 76
>   Non-zero exit status: 17
> t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
> t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: No plan found in TAP output
> t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 47 tests but ran 0.
> t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: No plan found in TAP output
> t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
> t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
> Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97 cusr  0.25
> csys =  2.28 CPU)
> Result: FAIL
> Failed 7/9 test programs. 17/90 subtests failed.
>   LDS/GBrowse-2.48.tar.gz
>   ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>   reports LDS/GBrowse-2.48.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store persistent
> state
> Running Build install
>   make test had returned bad status, won't install without force
>
>
>
>
>
>
>
> On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> What sort of errors?  Do you have developers tools like make and gcc
>> installed?
>>
>> Scott
>>
>> PS: I took the gmane list out of the cc list and added GBrowse.
>>
>> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> > I tried this command,
>> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
>> > on Ubuntu but returned errors on both Fedora & CentOS.
>> > What do you think?
>> >
>> > Thanks,
>> >
>> >
>> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]>
>> > wrote:
>> >>
>> >> Thanks Scott, I'll give it a try and get back to you
>> >>
>> >>
>> >>
>> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Hi Omar,
>> >>>
>> >>> From source/the cpan shell since there aren't RPMs for GBrowse (though
>> >>> there is a debian package that works with debian and ubuntu).  Also,
>> >>> if you can turn off SELinux it makes life easier.
>> >>>
>> >>> Scott
>> >>>
>> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish <[hidden email]>
>> >>> wrote:
>> >>> > Hello all,
>> >>> >
>> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>> >>> >
>> >>> > --
>> >>> > Thank you,
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> > ------------------------------------------------------------------------------
>> >>> > This SF email is sponsosred by:
>> >>> > Try Windows Azure free for 90 days Click Here
>> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >>> > _______________________________________________
>> >>> > 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
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Regards,
>> >> Omar
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

Yes, if you type "script" before entering the cpan shell, everything
you type and the responses on the screen are saved to a file.  To make
script quit, you type control-D.

Scott


On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]> wrote:

> Oh, I am not really sure about your question, Is there any way (command) i
> can save the installation output to a file so that i can send it to you ?
>
> Thanks
>
>
> On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> That is a pretty massive failure--it looks like all of the tests
>> failed to even run.  Did the prerequisites installed with the cpan
>> shell install properly?
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Below the last lines i got from the Installation process, I am not sure
>> > if
>> > they can help:
>> >
>> > Test Summary Report
>> > -------------------
>> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >                 36, 40, 42, 47, 76
>> >   Non-zero exit status: 17
>> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: No plan found in TAP output
>> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: No plan found in TAP output
>> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97 cusr
>> >  0.25
>> > csys =  2.28 CPU)
>> > Result: FAIL
>> > Failed 7/9 test programs. 17/90 subtests failed.
>> >   LDS/GBrowse-2.48.tar.gz
>> >   ./Build test -- NOT OK
>> > //hint// to see the cpan-testers results for installing this module,
>> > try:
>> >   reports LDS/GBrowse-2.48.tar.gz
>> > Warning (usually harmless): 'YAML' not installed, will not store
>> > persistent
>> > state
>> > Running Build install
>> >   make test had returned bad status, won't install without force
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> What sort of errors?  Do you have developers tools like make and gcc
>> >> installed?
>> >>
>> >> Scott
>> >>
>> >> PS: I took the gmane list out of the cc list and added GBrowse.
>> >>
>> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> > I tried this command,
>> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
>> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> > What do you think?
>> >> >
>> >> > Thanks,
>> >> >
>> >> >
>> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> >> wrote:
>> >> >>>
>> >> >>> Hi Omar,
>> >> >>>
>> >> >>> From source/the cpan shell since there aren't RPMs for GBrowse
>> >> >>> (though
>> >> >>> there is a debian package that works with debian and ubuntu).
>> >> >>>  Also,
>> >> >>> if you can turn off SELinux it makes life easier.
>> >> >>>
>> >> >>> Scott
>> >> >>>
>> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >>> <[hidden email]>
>> >> >>> wrote:
>> >> >>> > Hello all,
>> >> >>> >
>> >> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>> >> >>> >
>> >> >>> > --
>> >> >>> > Thank you,
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> > ------------------------------------------------------------------------------
>> >> >>> > This SF email is sponsosred by:
>> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >>> > _______________________________________________
>> >> >>> > 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
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Regards,
>> >> >> Omar
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Omar Darwish
Hi Scott,
Please see the attached file

On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

Yes, if you type "script" before entering the cpan shell, everything
you type and the responses on the screen are saved to a file.  To make
script quit, you type control-D.

Scott


On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]> wrote:
> Oh, I am not really sure about your question, Is there any way (command) i
> can save the installation output to a file so that i can send it to you ?
>
> Thanks
>
>
> On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> That is a pretty massive failure--it looks like all of the tests
>> failed to even run.  Did the prerequisites installed with the cpan
>> shell install properly?
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Below the last lines i got from the Installation process, I am not sure
>> > if
>> > they can help:
>> >
>> > Test Summary Report
>> > -------------------
>> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >                 36, 40, 42, 47, 76
>> >   Non-zero exit status: 17
>> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: No plan found in TAP output
>> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: No plan found in TAP output
>> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >   Non-zero exit status: 2
>> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97 cusr
>> >  0.25
>> > csys =  2.28 CPU)
>> > Result: FAIL
>> > Failed 7/9 test programs. 17/90 subtests failed.
>> >   LDS/GBrowse-2.48.tar.gz
>> >   ./Build test -- NOT OK
>> > //hint// to see the cpan-testers results for installing this module,
>> > try:
>> >   reports LDS/GBrowse-2.48.tar.gz
>> > Warning (usually harmless): 'YAML' not installed, will not store
>> > persistent
>> > state
>> > Running Build install
>> >   make test had returned bad status, won't install without force
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> What sort of errors?  Do you have developers tools like make and gcc
>> >> installed?
>> >>
>> >> Scott
>> >>
>> >> PS: I took the gmane list out of the cc list and added GBrowse.
>> >>
>> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> > I tried this command,
>> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It worked
>> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> > What do you think?
>> >> >
>> >> > Thanks,
>> >> >
>> >> >
>> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> >> wrote:
>> >> >>>
>> >> >>> Hi Omar,
>> >> >>>
>> >> >>> From source/the cpan shell since there aren't RPMs for GBrowse
>> >> >>> (though
>> >> >>> there is a debian package that works with debian and ubuntu).
>> >> >>>  Also,
>> >> >>> if you can turn off SELinux it makes life easier.
>> >> >>>
>> >> >>> Scott
>> >> >>>
>> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >>> <[hidden email]>
>> >> >>> wrote:
>> >> >>> > Hello all,
>> >> >>> >
>> >> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora ??
>> >> >>> >
>> >> >>> > --
>> >> >>> > Thank you,
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> > ------------------------------------------------------------------------------
>> >> >>> > This SF email is sponsosred by:
>> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >>> > _______________________________________________
>> >> >>> > 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
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Regards,
>> >> >> Omar
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> 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
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

------------------------------------------------------------------------------
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typescript.txt (124K) Download Attachment
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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

Bio::Graphics isn't getting installed since GD won't install.  GD
won't install because you don't have the libgd headers installed.  The
easiest thing to do would be to use yum to install GD:

  sudo yum install perl-GD

but to do that you might have to add rpmforge as a yum repository.  See:

  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge

Scott


On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]> wrote:

> Hi Scott,
> Please see the attached file
>
>
> On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Yes, if you type "script" before entering the cpan shell, everything
>> you type and the responses on the screen are saved to a file.  To make
>> script quit, you type control-D.
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Oh, I am not really sure about your question, Is there any way (command)
>> > i
>> > can save the installation output to a file so that i can send it to you
>> > ?
>> >
>> > Thanks
>> >
>> >
>> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> That is a pretty massive failure--it looks like all of the tests
>> >> failed to even run.  Did the prerequisites installed with the cpan
>> >> shell install properly?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Below the last lines i got from the Installation process, I am not
>> >> > sure
>> >> > if
>> >> > they can help:
>> >> >
>> >> > Test Summary Report
>> >> > -------------------
>> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >                 36, 40, 42, 47, 76
>> >> >   Non-zero exit status: 17
>> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: No plan found in TAP output
>> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: No plan found in TAP output
>> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97
>> >> > cusr
>> >> >  0.25
>> >> > csys =  2.28 CPU)
>> >> > Result: FAIL
>> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >   ./Build test -- NOT OK
>> >> > //hint// to see the cpan-testers results for installing this module,
>> >> > try:
>> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> > Warning (usually harmless): 'YAML' not installed, will not store
>> >> > persistent
>> >> > state
>> >> > Running Build install
>> >> >   make test had returned bad status, won't install without force
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> What sort of errors?  Do you have developers tools like make and gcc
>> >> >> installed?
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >> PS: I took the gmane list out of the cc list and added GBrowse.
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Hi Scott,
>> >> >> > I tried this command,
>> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It
>> >> >> > worked
>> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> > What do you think?
>> >> >> >
>> >> >> > Thanks,
>> >> >> >
>> >> >> >
>> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> > <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> >> >> wrote:
>> >> >> >>>
>> >> >> >>> Hi Omar,
>> >> >> >>>
>> >> >> >>> From source/the cpan shell since there aren't RPMs for GBrowse
>> >> >> >>> (though
>> >> >> >>> there is a debian package that works with debian and ubuntu).
>> >> >> >>>  Also,
>> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >>>
>> >> >> >>> Scott
>> >> >> >>>
>> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >>> <[hidden email]>
>> >> >> >>> wrote:
>> >> >> >>> > Hello all,
>> >> >> >>> >
>> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora
>> >> >> >>> > ??
>> >> >> >>> >
>> >> >> >>> > --
>> >> >> >>> > Thank you,
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >>> > This SF email is sponsosred by:
>> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >>> > _______________________________________________
>> >> >> >>> > 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
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Regards,
>> >> >> >> Omar
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Omar Darwish
Hi Scott,

I installed the Bio::Graphics, it went fine i guess, please take a look at the new attached output file

Thanks

On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

Bio::Graphics isn't getting installed since GD won't install.  GD
won't install because you don't have the libgd headers installed.  The
easiest thing to do would be to use yum to install GD:

 sudo yum install perl-GD

but to do that you might have to add rpmforge as a yum repository.  See:

 http://wiki.centos.org/AdditionalResources/Repositories/RPMForge

Scott


On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]> wrote:
> Hi Scott,
> Please see the attached file
>
>
> On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Yes, if you type "script" before entering the cpan shell, everything
>> you type and the responses on the screen are saved to a file.  To make
>> script quit, you type control-D.
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Oh, I am not really sure about your question, Is there any way (command)
>> > i
>> > can save the installation output to a file so that i can send it to you
>> > ?
>> >
>> > Thanks
>> >
>> >
>> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> That is a pretty massive failure--it looks like all of the tests
>> >> failed to even run.  Did the prerequisites installed with the cpan
>> >> shell install properly?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Below the last lines i got from the Installation process, I am not
>> >> > sure
>> >> > if
>> >> > they can help:
>> >> >
>> >> > Test Summary Report
>> >> > -------------------
>> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >                 36, 40, 42, 47, 76
>> >> >   Non-zero exit status: 17
>> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: No plan found in TAP output
>> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: No plan found in TAP output
>> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >   Non-zero exit status: 2
>> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97
>> >> > cusr
>> >> >  0.25
>> >> > csys =  2.28 CPU)
>> >> > Result: FAIL
>> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >   ./Build test -- NOT OK
>> >> > //hint// to see the cpan-testers results for installing this module,
>> >> > try:
>> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> > Warning (usually harmless): 'YAML' not installed, will not store
>> >> > persistent
>> >> > state
>> >> > Running Build install
>> >> >   make test had returned bad status, won't install without force
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> What sort of errors?  Do you have developers tools like make and gcc
>> >> >> installed?
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >> PS: I took the gmane list out of the cc list and added GBrowse.
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Hi Scott,
>> >> >> > I tried this command,
>> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It
>> >> >> > worked
>> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> > What do you think?
>> >> >> >
>> >> >> > Thanks,
>> >> >> >
>> >> >> >
>> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> > <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain <[hidden email]>
>> >> >> >> wrote:
>> >> >> >>>
>> >> >> >>> Hi Omar,
>> >> >> >>>
>> >> >> >>> From source/the cpan shell since there aren't RPMs for GBrowse
>> >> >> >>> (though
>> >> >> >>> there is a debian package that works with debian and ubuntu).
>> >> >> >>>  Also,
>> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >>>
>> >> >> >>> Scott
>> >> >> >>>
>> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >>> <[hidden email]>
>> >> >> >>> wrote:
>> >> >> >>> > Hello all,
>> >> >> >>> >
>> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS & Fedora
>> >> >> >>> > ??
>> >> >> >>> >
>> >> >> >>> > --
>> >> >> >>> > Thank you,
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >>> > This SF email is sponsosred by:
>> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >>> > _______________________________________________
>> >> >> >>> > 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
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Regards,
>> >> >> >> Omar
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> 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
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> 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
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

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typescript2.txt (77K) Download Attachment
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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

While you shouldn't need (and didn't used to need) the perl module DBI
to install GBrowse, apparently something has changed recently.  If you
install perl-DBI with yum things should work.  In reality, unless you
are just installing GBrowse to do the tutorial and nothing else,
you're going to want DBI anyway.

Scott


On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish <[hidden email]> wrote:

> Hi Scott,
>
> I installed the Bio::Graphics, it went fine i guess, please take a look at
> the new attached output file
>
> Thanks
>
>
> On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Bio::Graphics isn't getting installed since GD won't install.  GD
>> won't install because you don't have the libgd headers installed.  The
>> easiest thing to do would be to use yum to install GD:
>>
>>  sudo yum install perl-GD
>>
>> but to do that you might have to add rpmforge as a yum repository.  See:
>>
>>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> > Please see the attached file
>> >
>> >
>> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> Yes, if you type "script" before entering the cpan shell, everything
>> >> you type and the responses on the screen are saved to a file.  To make
>> >> script quit, you type control-D.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Oh, I am not really sure about your question, Is there any way
>> >> > (command)
>> >> > i
>> >> > can save the installation output to a file so that i can send it to
>> >> > you
>> >> > ?
>> >> >
>> >> > Thanks
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> That is a pretty massive failure--it looks like all of the tests
>> >> >> failed to even run.  Did the prerequisites installed with the cpan
>> >> >> shell install properly?
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Below the last lines i got from the Installation process, I am not
>> >> >> > sure
>> >> >> > if
>> >> >> > they can help:
>> >> >> >
>> >> >> > Test Summary Report
>> >> >> > -------------------
>> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >> >                 36, 40, 42, 47, 76
>> >> >> >   Non-zero exit status: 17
>> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: No plan found in TAP output
>> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: No plan found in TAP output
>> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >   Non-zero exit status: 2
>> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +  1.97
>> >> >> > cusr
>> >> >> >  0.25
>> >> >> > csys =  2.28 CPU)
>> >> >> > Result: FAIL
>> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >   ./Build test -- NOT OK
>> >> >> > //hint// to see the cpan-testers results for installing this
>> >> >> > module,
>> >> >> > try:
>> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> > Warning (usually harmless): 'YAML' not installed, will not store
>> >> >> > persistent
>> >> >> > state
>> >> >> > Running Build install
>> >> >> >   make test had returned bad status, won't install without force
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> What sort of errors?  Do you have developers tools like make and
>> >> >> >> gcc
>> >> >> >> installed?
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >> PS: I took the gmane list out of the cc list and added GBrowse.
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Hi Scott,
>> >> >> >> > I tried this command,
>> >> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It
>> >> >> >> > worked
>> >> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> >> > What do you think?
>> >> >> >> >
>> >> >> >> > Thanks,
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >>>
>> >> >> >> >>> Hi Omar,
>> >> >> >> >>>
>> >> >> >> >>> From source/the cpan shell since there aren't RPMs for
>> >> >> >> >>> GBrowse
>> >> >> >> >>> (though
>> >> >> >> >>> there is a debian package that works with debian and ubuntu).
>> >> >> >> >>>  Also,
>> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >>>
>> >> >> >> >>> Scott
>> >> >> >> >>>
>> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >>> <[hidden email]>
>> >> >> >> >>> wrote:
>> >> >> >> >>> > Hello all,
>> >> >> >> >>> >
>> >> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS &
>> >> >> >> >>> > Fedora
>> >> >> >> >>> > ??
>> >> >> >> >>> >
>> >> >> >> >>> > --
>> >> >> >> >>> > Thank you,
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> >
>> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >>> > _______________________________________________
>> >> >> >> >>> > 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
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >> Regards,
>> >> >> >> >> Omar
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



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

------------------------------------------------------------------------------
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure
_______________________________________________
Gmod-gbrowse mailing list
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|

Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

I just looked back at the installation log that you sent--the
installer suggested that you install in /usr/local/apache, which is
where it would be if you built apache from source, which I'm guessing
you didn't do.  The easiest way to fix that is to "rm -rf
/usr/local/apache" and force the installation of GBrowse again:

  sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

The reason that happened is you tried to install GBrowse before you
installed apache, and when the installer didn't find the directories
for the system installed apache, it assumed you must have one you
installed yourself, and created /usr/local/apache and put the GBrowse
files there.  (A possible second explanation is that CentOS changed
where it's apache directories are, but I don't think that is it since
I probably would have heard about it by now.)

Scott


On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]> wrote:

> Thanks Scott, I guess it worked After installing perl DBI!!
> To double check, i tried executing ( sudo perl -MCPAN -e 'install
> Bio::Graphics::Browser2' ) one more time, it returned the lines below:
> CPAN: Storable loaded ok (v2.20)
> Going to read '/root/.cpan/Metadata'
>   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
> Bio::Graphics::Browser2 is up to date (2.48).
>
>
> Apache server is running, I tried to access (http://localhost/gbrowse2) I
> got page Not Found
> Do I need to do any kind of configuration ?
>
> Regards
>
>
>
>
> On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> While you shouldn't need (and didn't used to need) the perl module DBI
>> to install GBrowse, apparently something has changed recently.  If you
>> install perl-DBI with yum things should work.  In reality, unless you
>> are just installing GBrowse to do the tutorial and nothing else,
>> you're going to want DBI anyway.
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> >
>> > I installed the Bio::Graphics, it went fine i guess, please take a look
>> > at
>> > the new attached output file
>> >
>> > Thanks
>> >
>> >
>> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> Bio::Graphics isn't getting installed since GD won't install.  GD
>> >> won't install because you don't have the libgd headers installed.  The
>> >> easiest thing to do would be to use yum to install GD:
>> >>
>> >>  sudo yum install perl-GD
>> >>
>> >> but to do that you might have to add rpmforge as a yum repository.
>> >>  See:
>> >>
>> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> > Please see the attached file
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> Yes, if you type "script" before entering the cpan shell, everything
>> >> >> you type and the responses on the screen are saved to a file.  To
>> >> >> make
>> >> >> script quit, you type control-D.
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Oh, I am not really sure about your question, Is there any way
>> >> >> > (command)
>> >> >> > i
>> >> >> > can save the installation output to a file so that i can send it
>> >> >> > to
>> >> >> > you
>> >> >> > ?
>> >> >> >
>> >> >> > Thanks
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> That is a pretty massive failure--it looks like all of the tests
>> >> >> >> failed to even run.  Did the prerequisites installed with the
>> >> >> >> cpan
>> >> >> >> shell install properly?
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Below the last lines i got from the Installation process, I am
>> >> >> >> > not
>> >> >> >> > sure
>> >> >> >> > if
>> >> >> >> > they can help:
>> >> >> >> >
>> >> >> >> > Test Summary Report
>> >> >> >> > -------------------
>> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >   Non-zero exit status: 17
>> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +
>> >> >> >> >  1.97
>> >> >> >> > cusr
>> >> >> >> >  0.25
>> >> >> >> > csys =  2.28 CPU)
>> >> >> >> > Result: FAIL
>> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> > //hint// to see the cpan-testers results for installing this
>> >> >> >> > module,
>> >> >> >> > try:
>> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> > Warning (usually harmless): 'YAML' not installed, will not
>> >> >> >> > store
>> >> >> >> > persistent
>> >> >> >> > state
>> >> >> >> > Running Build install
>> >> >> >> >   make test had returned bad status, won't install without
>> >> >> >> > force
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> What sort of errors?  Do you have developers tools like make
>> >> >> >> >> and
>> >> >> >> >> gcc
>> >> >> >> >> installed?
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >> PS: I took the gmane list out of the cc list and added
>> >> >> >> >> GBrowse.
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Hi Scott,
>> >> >> >> >> > I tried this command,
>> >> >> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It
>> >> >> >> >> > worked
>> >> >> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> >> >> > What do you think?
>> >> >> >> >> >
>> >> >> >> >> > Thanks,
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >>>
>> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >>>
>> >> >> >> >> >>> From source/the cpan shell since there aren't RPMs for
>> >> >> >> >> >>> GBrowse
>> >> >> >> >> >>> (though
>> >> >> >> >> >>> there is a debian package that works with debian and
>> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >>>  Also,
>> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >>>
>> >> >> >> >> >>> Scott
>> >> >> >> >> >>>
>> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >>> wrote:
>> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS &
>> >> >> >> >> >>> > Fedora
>> >> >> >> >> >>> > ??
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > --
>> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >>> > 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
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >> Regards,
>> >> >> >> >> >> Omar
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> >> scottcain
>> >> >> >> >> dot net
>> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> 216-392-3087
>> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Omar Darwish
Hi Scott,

I could not find this directory /usr/local/apache ?? i can only see is this one /etc/httpd 



On Wed, Mar 28, 2012 at 4:48 PM, Scott Cain <[hidden email]> wrote:
Hi Omar,

I just looked back at the installation log that you sent--the
installer suggested that you install in /usr/local/apache, which is
where it would be if you built apache from source, which I'm guessing
you didn't do.  The easiest way to fix that is to "rm -rf
/usr/local/apache" and force the installation of GBrowse again:

 sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

The reason that happened is you tried to install GBrowse before you
installed apache, and when the installer didn't find the directories
for the system installed apache, it assumed you must have one you
installed yourself, and created /usr/local/apache and put the GBrowse
files there.  (A possible second explanation is that CentOS changed
where it's apache directories are, but I don't think that is it since
I probably would have heard about it by now.)

Scott


On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]> wrote:
> Thanks Scott, I guess it worked After installing perl DBI!!
> To double check, i tried executing ( sudo perl -MCPAN -e 'install
> Bio::Graphics::Browser2' ) one more time, it returned the lines below:
> CPAN: Storable loaded ok (v2.20)
> Going to read '/root/.cpan/Metadata'
>   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
> Bio::Graphics::Browser2 is up to date (2.48).
>
>
> Apache server is running, I tried to access (http://localhost/gbrowse2) I
> got page Not Found
> Do I need to do any kind of configuration ?
>
> Regards
>
>
>
>
> On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> While you shouldn't need (and didn't used to need) the perl module DBI
>> to install GBrowse, apparently something has changed recently.  If you
>> install perl-DBI with yum things should work.  In reality, unless you
>> are just installing GBrowse to do the tutorial and nothing else,
>> you're going to want DBI anyway.
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> >
>> > I installed the Bio::Graphics, it went fine i guess, please take a look
>> > at
>> > the new attached output file
>> >
>> > Thanks
>> >
>> >
>> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> Bio::Graphics isn't getting installed since GD won't install.  GD
>> >> won't install because you don't have the libgd headers installed.  The
>> >> easiest thing to do would be to use yum to install GD:
>> >>
>> >>  sudo yum install perl-GD
>> >>
>> >> but to do that you might have to add rpmforge as a yum repository.
>> >>  See:
>> >>
>> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> > Please see the attached file
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> Yes, if you type "script" before entering the cpan shell, everything
>> >> >> you type and the responses on the screen are saved to a file.  To
>> >> >> make
>> >> >> script quit, you type control-D.
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Oh, I am not really sure about your question, Is there any way
>> >> >> > (command)
>> >> >> > i
>> >> >> > can save the installation output to a file so that i can send it
>> >> >> > to
>> >> >> > you
>> >> >> > ?
>> >> >> >
>> >> >> > Thanks
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> That is a pretty massive failure--it looks like all of the tests
>> >> >> >> failed to even run.  Did the prerequisites installed with the
>> >> >> >> cpan
>> >> >> >> shell install properly?
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Below the last lines i got from the Installation process, I am
>> >> >> >> > not
>> >> >> >> > sure
>> >> >> >> > if
>> >> >> >> > they can help:
>> >> >> >> >
>> >> >> >> > Test Summary Report
>> >> >> >> > -------------------
>> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >   Non-zero exit status: 17
>> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +
>> >> >> >> >  1.97
>> >> >> >> > cusr
>> >> >> >> >  0.25
>> >> >> >> > csys =  2.28 CPU)
>> >> >> >> > Result: FAIL
>> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> > //hint// to see the cpan-testers results for installing this
>> >> >> >> > module,
>> >> >> >> > try:
>> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> > Warning (usually harmless): 'YAML' not installed, will not
>> >> >> >> > store
>> >> >> >> > persistent
>> >> >> >> > state
>> >> >> >> > Running Build install
>> >> >> >> >   make test had returned bad status, won't install without
>> >> >> >> > force
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> What sort of errors?  Do you have developers tools like make
>> >> >> >> >> and
>> >> >> >> >> gcc
>> >> >> >> >> installed?
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >> PS: I took the gmane list out of the cc list and added
>> >> >> >> >> GBrowse.
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Hi Scott,
>> >> >> >> >> > I tried this command,
>> >> >> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ... It
>> >> >> >> >> > worked
>> >> >> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> >> >> > What do you think?
>> >> >> >> >> >
>> >> >> >> >> > Thanks,
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >>>
>> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >>>
>> >> >> >> >> >>> From source/the cpan shell since there aren't RPMs for
>> >> >> >> >> >>> GBrowse
>> >> >> >> >> >>> (though
>> >> >> >> >> >>> there is a debian package that works with debian and
>> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >>>  Also,
>> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >>>
>> >> >> >> >> >>> Scott
>> >> >> >> >> >>>
>> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >>> wrote:
>> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS &
>> >> >> >> >> >>> > Fedora
>> >> >> >> >> >>> > ??
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > --
>> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> >
>> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >>> > 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
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >> Regards,
>> >> >> >> >> >> Omar
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> 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
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> 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
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> 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
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> 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
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

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Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

Well then I guessed wrong what the problem was.  Does /var/www exist?
Does it have an html directory, and a gbrowse2 directory in it?

Scott


On Wed, Mar 28, 2012 at 5:07 PM, Omar Darwish <[hidden email]> wrote:

> Hi Scott,
>
> I could not find this directory /usr/local/apache ?? i can only see is this
> one /etc/httpd
>
>
>
> On Wed, Mar 28, 2012 at 4:48 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> I just looked back at the installation log that you sent--the
>> installer suggested that you install in /usr/local/apache, which is
>> where it would be if you built apache from source, which I'm guessing
>> you didn't do.  The easiest way to fix that is to "rm -rf
>> /usr/local/apache" and force the installation of GBrowse again:
>>
>>  sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'
>>
>> The reason that happened is you tried to install GBrowse before you
>> installed apache, and when the installer didn't find the directories
>> for the system installed apache, it assumed you must have one you
>> installed yourself, and created /usr/local/apache and put the GBrowse
>> files there.  (A possible second explanation is that CentOS changed
>> where it's apache directories are, but I don't think that is it since
>> I probably would have heard about it by now.)
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Thanks Scott, I guess it worked After installing perl DBI!!
>> > To double check, i tried executing ( sudo perl -MCPAN -e 'install
>> > Bio::Graphics::Browser2' ) one more time, it returned the lines below:
>> > CPAN: Storable loaded ok (v2.20)
>> > Going to read '/root/.cpan/Metadata'
>> >   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
>> > Bio::Graphics::Browser2 is up to date (2.48).
>> >
>> >
>> > Apache server is running, I tried to access (http://localhost/gbrowse2)
>> > I
>> > got page Not Found
>> > Do I need to do any kind of configuration ?
>> >
>> > Regards
>> >
>> >
>> >
>> >
>> > On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> While you shouldn't need (and didn't used to need) the perl module DBI
>> >> to install GBrowse, apparently something has changed recently.  If you
>> >> install perl-DBI with yum things should work.  In reality, unless you
>> >> are just installing GBrowse to do the tutorial and nothing else,
>> >> you're going to want DBI anyway.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > I installed the Bio::Graphics, it went fine i guess, please take a
>> >> > look
>> >> > at
>> >> > the new attached output file
>> >> >
>> >> > Thanks
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> Bio::Graphics isn't getting installed since GD won't install.  GD
>> >> >> won't install because you don't have the libgd headers installed.
>> >> >>  The
>> >> >> easiest thing to do would be to use yum to install GD:
>> >> >>
>> >> >>  sudo yum install perl-GD
>> >> >>
>> >> >> but to do that you might have to add rpmforge as a yum repository.
>> >> >>  See:
>> >> >>
>> >> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Hi Scott,
>> >> >> > Please see the attached file
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> Yes, if you type "script" before entering the cpan shell,
>> >> >> >> everything
>> >> >> >> you type and the responses on the screen are saved to a file.  To
>> >> >> >> make
>> >> >> >> script quit, you type control-D.
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Oh, I am not really sure about your question, Is there any way
>> >> >> >> > (command)
>> >> >> >> > i
>> >> >> >> > can save the installation output to a file so that i can send
>> >> >> >> > it
>> >> >> >> > to
>> >> >> >> > you
>> >> >> >> > ?
>> >> >> >> >
>> >> >> >> > Thanks
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> That is a pretty massive failure--it looks like all of the
>> >> >> >> >> tests
>> >> >> >> >> failed to even run.  Did the prerequisites installed with the
>> >> >> >> >> cpan
>> >> >> >> >> shell install properly?
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Below the last lines i got from the Installation process, I
>> >> >> >> >> > am
>> >> >> >> >> > not
>> >> >> >> >> > sure
>> >> >> >> >> > if
>> >> >> >> >> > they can help:
>> >> >> >> >> >
>> >> >> >> >> > Test Summary Report
>> >> >> >> >> > -------------------
>> >> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed: 17)
>> >> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32, 34
>> >> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >> >   Non-zero exit status: 17
>> >> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>> >> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but ran 0.
>> >> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>> >> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys +
>> >> >> >> >> >  1.97
>> >> >> >> >> > cusr
>> >> >> >> >> >  0.25
>> >> >> >> >> > csys =  2.28 CPU)
>> >> >> >> >> > Result: FAIL
>> >> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> >> > //hint// to see the cpan-testers results for installing this
>> >> >> >> >> > module,
>> >> >> >> >> > try:
>> >> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> > Warning (usually harmless): 'YAML' not installed, will not
>> >> >> >> >> > store
>> >> >> >> >> > persistent
>> >> >> >> >> > state
>> >> >> >> >> > Running Build install
>> >> >> >> >> >   make test had returned bad status, won't install without
>> >> >> >> >> > force
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >>
>> >> >> >> >> >> What sort of errors?  Do you have developers tools like
>> >> >> >> >> >> make
>> >> >> >> >> >> and
>> >> >> >> >> >> gcc
>> >> >> >> >> >> installed?
>> >> >> >> >> >>
>> >> >> >> >> >> Scott
>> >> >> >> >> >>
>> >> >> >> >> >> PS: I took the gmane list out of the cc list and added
>> >> >> >> >> >> GBrowse.
>> >> >> >> >> >>
>> >> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >> > Hi Scott,
>> >> >> >> >> >> > I tried this command,
>> >> >> >> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' ...
>> >> >> >> >> >> > It
>> >> >> >> >> >> > worked
>> >> >> >> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> >> >> >> > What do you think?
>> >> >> >> >> >> >
>> >> >> >> >> >> > Thanks,
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >>>
>> >> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >> >>>
>> >> >> >> >> >> >>> From source/the cpan shell since there aren't RPMs for
>> >> >> >> >> >> >>> GBrowse
>> >> >> >> >> >> >>> (though
>> >> >> >> >> >> >>> there is a debian package that works with debian and
>> >> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >> >>>  Also,
>> >> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >> >>>
>> >> >> >> >> >> >>> Scott
>> >> >> >> >> >> >>>
>> >> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >> >>> wrote:
>> >> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on CentOS
>> >> >> >> >> >> >>> > &
>> >> >> >> >> >> >>> > Fedora
>> >> >> >> >> >> >>> > ??
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> > --
>> >> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> >
>> >> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >> >>> > 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
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> --
>> >> >> >> >> >> >> Regards,
>> >> >> >> >> >> >> Omar
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > --
>> >> >> >> >> >> > Regards,
>> >> >> >> >> >> > Omar
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> Scott Cain, Ph. D.                                   scott
>> >> >> >> >> >> at
>> >> >> >> >> >> scottcain
>> >> >> >> >> >> dot net
>> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> >> scottcain
>> >> >> >> >> dot net
>> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> 216-392-3087
>> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



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

------------------------------------------------------------------------------
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure
_______________________________________________
Gmod-gbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Gbrowse installation on CentOS

Scott Cain
Hi Omar,

Is the gbrowse2 directory in /var/www/html?

Scott

(please leave the GBrowse list cc'ed so the debugging can be archived)


On Wed, Mar 28, 2012 at 5:21 PM, Omar Darwish <[hidden email]> wrote:

> Yes, /var/www exists and it has (html, error, cgi-bin and icons)
>
>
> On Wed, Mar 28, 2012 at 5:11 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Well then I guessed wrong what the problem was.  Does /var/www exist?
>> Does it have an html directory, and a gbrowse2 directory in it?
>>
>> Scott
>>
>>
>> On Wed, Mar 28, 2012 at 5:07 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Hi Scott,
>> >
>> > I could not find this directory /usr/local/apache ?? i can only see is
>> > this
>> > one /etc/httpd
>> >
>> >
>> >
>> > On Wed, Mar 28, 2012 at 4:48 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> I just looked back at the installation log that you sent--the
>> >> installer suggested that you install in /usr/local/apache, which is
>> >> where it would be if you built apache from source, which I'm guessing
>> >> you didn't do.  The easiest way to fix that is to "rm -rf
>> >> /usr/local/apache" and force the installation of GBrowse again:
>> >>
>> >>  sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'
>> >>
>> >> The reason that happened is you tried to install GBrowse before you
>> >> installed apache, and when the installer didn't find the directories
>> >> for the system installed apache, it assumed you must have one you
>> >> installed yourself, and created /usr/local/apache and put the GBrowse
>> >> files there.  (A possible second explanation is that CentOS changed
>> >> where it's apache directories are, but I don't think that is it since
>> >> I probably would have heard about it by now.)
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Thanks Scott, I guess it worked After installing perl DBI!!
>> >> > To double check, i tried executing ( sudo perl -MCPAN -e 'install
>> >> > Bio::Graphics::Browser2' ) one more time, it returned the lines
>> >> > below:
>> >> > CPAN: Storable loaded ok (v2.20)
>> >> > Going to read '/root/.cpan/Metadata'
>> >> >   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
>> >> > Bio::Graphics::Browser2 is up to date (2.48).
>> >> >
>> >> >
>> >> > Apache server is running, I tried to access
>> >> > (http://localhost/gbrowse2)
>> >> > I
>> >> > got page Not Found
>> >> > Do I need to do any kind of configuration ?
>> >> >
>> >> > Regards
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> While you shouldn't need (and didn't used to need) the perl module
>> >> >> DBI
>> >> >> to install GBrowse, apparently something has changed recently.  If
>> >> >> you
>> >> >> install perl-DBI with yum things should work.  In reality, unless
>> >> >> you
>> >> >> are just installing GBrowse to do the tutorial and nothing else,
>> >> >> you're going to want DBI anyway.
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Hi Scott,
>> >> >> >
>> >> >> > I installed the Bio::Graphics, it went fine i guess, please take a
>> >> >> > look
>> >> >> > at
>> >> >> > the new attached output file
>> >> >> >
>> >> >> > Thanks
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> Bio::Graphics isn't getting installed since GD won't install.  GD
>> >> >> >> won't install because you don't have the libgd headers installed.
>> >> >> >>  The
>> >> >> >> easiest thing to do would be to use yum to install GD:
>> >> >> >>
>> >> >> >>  sudo yum install perl-GD
>> >> >> >>
>> >> >> >> but to do that you might have to add rpmforge as a yum
>> >> >> >> repository.
>> >> >> >>  See:
>> >> >> >>
>> >> >> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Hi Scott,
>> >> >> >> > Please see the attached file
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> Yes, if you type "script" before entering the cpan shell,
>> >> >> >> >> everything
>> >> >> >> >> you type and the responses on the screen are saved to a file.
>> >> >> >> >>  To
>> >> >> >> >> make
>> >> >> >> >> script quit, you type control-D.
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Oh, I am not really sure about your question, Is there any
>> >> >> >> >> > way
>> >> >> >> >> > (command)
>> >> >> >> >> > i
>> >> >> >> >> > can save the installation output to a file so that i can
>> >> >> >> >> > send
>> >> >> >> >> > it
>> >> >> >> >> > to
>> >> >> >> >> > you
>> >> >> >> >> > ?
>> >> >> >> >> >
>> >> >> >> >> > Thanks
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >>
>> >> >> >> >> >> That is a pretty massive failure--it looks like all of the
>> >> >> >> >> >> tests
>> >> >> >> >> >> failed to even run.  Did the prerequisites installed with
>> >> >> >> >> >> the
>> >> >> >> >> >> cpan
>> >> >> >> >> >> shell install properly?
>> >> >> >> >> >>
>> >> >> >> >> >> Scott
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >> > Below the last lines i got from the Installation process,
>> >> >> >> >> >> > I
>> >> >> >> >> >> > am
>> >> >> >> >> >> > not
>> >> >> >> >> >> > sure
>> >> >> >> >> >> > if
>> >> >> >> >> >> > they can help:
>> >> >> >> >> >> >
>> >> >> >> >> >> > Test Summary Report
>> >> >> >> >> >> > -------------------
>> >> >> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed:
>> >> >> >> >> >> > 17)
>> >> >> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30, 32,
>> >> >> >> >> >> > 34
>> >> >> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >> >> >   Non-zero exit status: 17
>> >> >> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but ran
>> >> >> >> >> >> > 0.
>> >> >> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but ran
>> >> >> >> >> >> > 0.
>> >> >> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but ran
>> >> >> >> >> >> > 0.
>> >> >> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>> >> >> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02 sys
>> >> >> >> >> >> > +
>> >> >> >> >> >> >  1.97
>> >> >> >> >> >> > cusr
>> >> >> >> >> >> >  0.25
>> >> >> >> >> >> > csys =  2.28 CPU)
>> >> >> >> >> >> > Result: FAIL
>> >> >> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> >> >> > //hint// to see the cpan-testers results for installing
>> >> >> >> >> >> > this
>> >> >> >> >> >> > module,
>> >> >> >> >> >> > try:
>> >> >> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> > Warning (usually harmless): 'YAML' not installed, will
>> >> >> >> >> >> > not
>> >> >> >> >> >> > store
>> >> >> >> >> >> > persistent
>> >> >> >> >> >> > state
>> >> >> >> >> >> > Running Build install
>> >> >> >> >> >> >   make test had returned bad status, won't install
>> >> >> >> >> >> > without
>> >> >> >> >> >> > force
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> What sort of errors?  Do you have developers tools like
>> >> >> >> >> >> >> make
>> >> >> >> >> >> >> and
>> >> >> >> >> >> >> gcc
>> >> >> >> >> >> >> installed?
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Scott
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> PS: I took the gmane list out of the cc list and added
>> >> >> >> >> >> >> GBrowse.
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> > Hi Scott,
>> >> >> >> >> >> >> > I tried this command,
>> >> >> >> >> >> >> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >> >> >> >> >> > ...
>> >> >> >> >> >> >> > It
>> >> >> >> >> >> >> > worked
>> >> >> >> >> >> >> > on Ubuntu but returned errors on both Fedora & CentOS.
>> >> >> >> >> >> >> > What do you think?
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > Thanks,
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to you
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >>> From source/the cpan shell since there aren't RPMs
>> >> >> >> >> >> >> >>> for
>> >> >> >> >> >> >> >>> GBrowse
>> >> >> >> >> >> >> >>> (though
>> >> >> >> >> >> >> >>> there is a debian package that works with debian and
>> >> >> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >> >> >>>  Also,
>> >> >> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >>> Scott
>> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >> >> >>> wrote:
>> >> >> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on
>> >> >> >> >> >> >> >>> > CentOS
>> >> >> >> >> >> >> >>> > &
>> >> >> >> >> >> >> >>> > Fedora
>> >> >> >> >> >> >> >>> > ??
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> > --
>> >> >> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >> >> >>> > 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
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> --
>> >> >> >> >> >> >> >> Regards,
>> >> >> >> >> >> >> >> Omar
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > --
>> >> >> >> >> >> >> > Regards,
>> >> >> >> >> >> >> > Omar
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> --
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> >> Scott Cain, Ph. D.
>> >> >> >> >> >> >> scott
>> >> >> >> >> >> >> at
>> >> >> >> >> >> >> scottcain
>> >> >> >> >> >> >> dot net
>> >> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > --
>> >> >> >> >> >> > Regards,
>> >> >> >> >> >> > Omar
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> Scott Cain, Ph. D.                                   scott
>> >> >> >> >> >> at
>> >> >> >> >> >> scottcain
>> >> >> >> >> >> dot net
>> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> >> scottcain
>> >> >> >> >> dot net
>> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> 216-392-3087
>> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Scott Cain
Omar,

Are you familiar with the locate command?  Run updatedb and then try

  locate gbrowse2

to see where it went.

Scott


On Wed, Mar 28, 2012 at 5:23 PM, Omar Darwish <[hidden email]> wrote:

> Oh No it is empty!
>
>
> On Wed, Mar 28, 2012 at 5:22 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Is the gbrowse2 directory in /var/www/html?
>>
>> Scott
>>
>> (please leave the GBrowse list cc'ed so the debugging can be archived)
>>
>>
>> On Wed, Mar 28, 2012 at 5:21 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Yes, /var/www exists and it has (html, error, cgi-bin and icons)
>> >
>> >
>> > On Wed, Mar 28, 2012 at 5:11 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> Well then I guessed wrong what the problem was.  Does /var/www exist?
>> >> Does it have an html directory, and a gbrowse2 directory in it?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 5:07 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > I could not find this directory /usr/local/apache ?? i can only see
>> >> > is
>> >> > this
>> >> > one /etc/httpd
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 4:48 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> I just looked back at the installation log that you sent--the
>> >> >> installer suggested that you install in /usr/local/apache, which is
>> >> >> where it would be if you built apache from source, which I'm
>> >> >> guessing
>> >> >> you didn't do.  The easiest way to fix that is to "rm -rf
>> >> >> /usr/local/apache" and force the installation of GBrowse again:
>> >> >>
>> >> >>  sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'
>> >> >>
>> >> >> The reason that happened is you tried to install GBrowse before you
>> >> >> installed apache, and when the installer didn't find the directories
>> >> >> for the system installed apache, it assumed you must have one you
>> >> >> installed yourself, and created /usr/local/apache and put the
>> >> >> GBrowse
>> >> >> files there.  (A possible second explanation is that CentOS changed
>> >> >> where it's apache directories are, but I don't think that is it
>> >> >> since
>> >> >> I probably would have heard about it by now.)
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Thanks Scott, I guess it worked After installing perl DBI!!
>> >> >> > To double check, i tried executing ( sudo perl -MCPAN -e 'install
>> >> >> > Bio::Graphics::Browser2' ) one more time, it returned the lines
>> >> >> > below:
>> >> >> > CPAN: Storable loaded ok (v2.20)
>> >> >> > Going to read '/root/.cpan/Metadata'
>> >> >> >   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
>> >> >> > Bio::Graphics::Browser2 is up to date (2.48).
>> >> >> >
>> >> >> >
>> >> >> > Apache server is running, I tried to access
>> >> >> > (http://localhost/gbrowse2)
>> >> >> > I
>> >> >> > got page Not Found
>> >> >> > Do I need to do any kind of configuration ?
>> >> >> >
>> >> >> > Regards
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> While you shouldn't need (and didn't used to need) the perl
>> >> >> >> module
>> >> >> >> DBI
>> >> >> >> to install GBrowse, apparently something has changed recently.
>> >> >> >>  If
>> >> >> >> you
>> >> >> >> install perl-DBI with yum things should work.  In reality, unless
>> >> >> >> you
>> >> >> >> are just installing GBrowse to do the tutorial and nothing else,
>> >> >> >> you're going to want DBI anyway.
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Hi Scott,
>> >> >> >> >
>> >> >> >> > I installed the Bio::Graphics, it went fine i guess, please
>> >> >> >> > take a
>> >> >> >> > look
>> >> >> >> > at
>> >> >> >> > the new attached output file
>> >> >> >> >
>> >> >> >> > Thanks
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> Bio::Graphics isn't getting installed since GD won't install.
>> >> >> >> >>  GD
>> >> >> >> >> won't install because you don't have the libgd headers
>> >> >> >> >> installed.
>> >> >> >> >>  The
>> >> >> >> >> easiest thing to do would be to use yum to install GD:
>> >> >> >> >>
>> >> >> >> >>  sudo yum install perl-GD
>> >> >> >> >>
>> >> >> >> >> but to do that you might have to add rpmforge as a yum
>> >> >> >> >> repository.
>> >> >> >> >>  See:
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Hi Scott,
>> >> >> >> >> > Please see the attached file
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >>
>> >> >> >> >> >> Yes, if you type "script" before entering the cpan shell,
>> >> >> >> >> >> everything
>> >> >> >> >> >> you type and the responses on the screen are saved to a
>> >> >> >> >> >> file.
>> >> >> >> >> >>  To
>> >> >> >> >> >> make
>> >> >> >> >> >> script quit, you type control-D.
>> >> >> >> >> >>
>> >> >> >> >> >> Scott
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >> > Oh, I am not really sure about your question, Is there
>> >> >> >> >> >> > any
>> >> >> >> >> >> > way
>> >> >> >> >> >> > (command)
>> >> >> >> >> >> > i
>> >> >> >> >> >> > can save the installation output to a file so that i can
>> >> >> >> >> >> > send
>> >> >> >> >> >> > it
>> >> >> >> >> >> > to
>> >> >> >> >> >> > you
>> >> >> >> >> >> > ?
>> >> >> >> >> >> >
>> >> >> >> >> >> > Thanks
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain
>> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> That is a pretty massive failure--it looks like all of
>> >> >> >> >> >> >> the
>> >> >> >> >> >> >> tests
>> >> >> >> >> >> >> failed to even run.  Did the prerequisites installed
>> >> >> >> >> >> >> with
>> >> >> >> >> >> >> the
>> >> >> >> >> >> >> cpan
>> >> >> >> >> >> >> shell install properly?
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Scott
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> > Below the last lines i got from the Installation
>> >> >> >> >> >> >> > process,
>> >> >> >> >> >> >> > I
>> >> >> >> >> >> >> > am
>> >> >> >> >> >> >> > not
>> >> >> >> >> >> >> > sure
>> >> >> >> >> >> >> > if
>> >> >> >> >> >> >> > they can help:
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > Test Summary Report
>> >> >> >> >> >> >> > -------------------
>> >> >> >> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed:
>> >> >> >> >> >> >> > 17)
>> >> >> >> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30,
>> >> >> >> >> >> >> > 32,
>> >> >> >> >> >> >> > 34
>> >> >> >> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >> >> >> >   Non-zero exit status: 17
>> >> >> >> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02
>> >> >> >> >> >> >> > sys
>> >> >> >> >> >> >> > +
>> >> >> >> >> >> >> >  1.97
>> >> >> >> >> >> >> > cusr
>> >> >> >> >> >> >> >  0.25
>> >> >> >> >> >> >> > csys =  2.28 CPU)
>> >> >> >> >> >> >> > Result: FAIL
>> >> >> >> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> >> >> >> > //hint// to see the cpan-testers results for
>> >> >> >> >> >> >> > installing
>> >> >> >> >> >> >> > this
>> >> >> >> >> >> >> > module,
>> >> >> >> >> >> >> > try:
>> >> >> >> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> >> > Warning (usually harmless): 'YAML' not installed, will
>> >> >> >> >> >> >> > not
>> >> >> >> >> >> >> > store
>> >> >> >> >> >> >> > persistent
>> >> >> >> >> >> >> > state
>> >> >> >> >> >> >> > Running Build install
>> >> >> >> >> >> >> >   make test had returned bad status, won't install
>> >> >> >> >> >> >> > without
>> >> >> >> >> >> >> > force
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> What sort of errors?  Do you have developers tools
>> >> >> >> >> >> >> >> like
>> >> >> >> >> >> >> >> make
>> >> >> >> >> >> >> >> and
>> >> >> >> >> >> >> >> gcc
>> >> >> >> >> >> >> >> installed?
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> Scott
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> PS: I took the gmane list out of the cc list and
>> >> >> >> >> >> >> >> added
>> >> >> >> >> >> >> >> GBrowse.
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> >> > Hi Scott,
>> >> >> >> >> >> >> >> > I tried this command,
>> >> >> >> >> >> >> >> > sudo perl -MCPAN -e 'install
>> >> >> >> >> >> >> >> > Bio::Graphics::Browser2'
>> >> >> >> >> >> >> >> > ...
>> >> >> >> >> >> >> >> > It
>> >> >> >> >> >> >> >> > worked
>> >> >> >> >> >> >> >> > on Ubuntu but returned errors on both Fedora &
>> >> >> >> >> >> >> >> > CentOS.
>> >> >> >> >> >> >> >> > What do you think?
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > Thanks,
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to
>> >> >> >> >> >> >> >> >> you
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> From source/the cpan shell since there aren't
>> >> >> >> >> >> >> >> >>> RPMs
>> >> >> >> >> >> >> >> >>> for
>> >> >> >> >> >> >> >> >>> GBrowse
>> >> >> >> >> >> >> >> >>> (though
>> >> >> >> >> >> >> >> >>> there is a debian package that works with debian
>> >> >> >> >> >> >> >> >>> and
>> >> >> >> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >> >> >> >>>  Also,
>> >> >> >> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> Scott
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >> >> >> >>> wrote:
>> >> >> >> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on
>> >> >> >> >> >> >> >> >>> > CentOS
>> >> >> >> >> >> >> >> >>> > &
>> >> >> >> >> >> >> >> >>> > Fedora
>> >> >> >> >> >> >> >> >>> > ??
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > --
>> >> >> >> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >> >> >> >>> > 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
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> --
>> >> >> >> >> >> >> >> >> Regards,
>> >> >> >> >> >> >> >> >> Omar
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > --
>> >> >> >> >> >> >> >> > Regards,
>> >> >> >> >> >> >> >> > Omar
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> --
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> >> >> Scott Cain, Ph. D.
>> >> >> >> >> >> >> >> scott
>> >> >> >> >> >> >> >> at
>> >> >> >> >> >> >> >> scottcain
>> >> >> >> >> >> >> >> dot net
>> >> >> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > --
>> >> >> >> >> >> >> > Regards,
>> >> >> >> >> >> >> > Omar
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> --
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> >> Scott Cain, Ph. D.
>> >> >> >> >> >> >> scott
>> >> >> >> >> >> >> at
>> >> >> >> >> >> >> scottcain
>> >> >> >> >> >> >> dot net
>> >> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > --
>> >> >> >> >> >> > Regards,
>> >> >> >> >> >> > Omar
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> Scott Cain, Ph. D.                                   scott
>> >> >> >> >> >> at
>> >> >> >> >> >> scottcain
>> >> >> >> >> >> dot net
>> >> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> >> 216-392-3087
>> >> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> >> scottcain
>> >> >> >> >> dot net
>> >> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> >> 216-392-3087
>> >> >> >> >> Ontario Institute for Cancer Research
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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: Gbrowse installation on CentOS

Omar Darwish
Sorry to keep bugging you with this, i really appreciate your help.
This is what i got:
/etc/gbrowse2
/etc/gbrowse2/GBrowse.conf
/etc/gbrowse2/MobyServices
/etc/gbrowse2/detail_select_menu.conf
/etc/gbrowse2/enzymes.txt
/etc/gbrowse2/languages
/etc/gbrowse2/log4perl.conf
/etc/gbrowse2/plugins
/etc/gbrowse2/pop_demo.conf
/etc/gbrowse2/slave_preload.conf
/etc/gbrowse2/submitter_plugin.conf
/etc/gbrowse2/synteny
/etc/gbrowse2/themes
/etc/gbrowse2/volvox.conf
/etc/gbrowse2/yeast_chr1+2.conf
/etc/gbrowse2/yeast_renderfarm.conf
/etc/gbrowse2/yeast_simple.conf
/etc/gbrowse2/MobyServices/GbrowseServices.PMS
/etc/gbrowse2/MobyServices/GbrowseServices.pm
/etc/gbrowse2/MobyServices/b64_encoded_gif_renderer.pm
/etc/gbrowse2/MobyServices/b64_encoded_jpeg_renderer.pm
/etc/gbrowse2/MobyServices/moby.conf
/etc/gbrowse2/MobyServices/text_formatted_renderer.pm
/etc/gbrowse2/MobyServices/text_html_renderer.pm
/etc/gbrowse2/MobyServices/text_plain_renderer.pm
/etc/gbrowse2/MobyServices/text_xml_renderer.pm
/etc/gbrowse2/languages/POSIX.pm
/etc/gbrowse2/languages/de.pm
/etc/gbrowse2/languages/en.pm
/etc/gbrowse2/languages/es.pm
/etc/gbrowse2/languages/fr.pm
/etc/gbrowse2/languages/is.pm
/etc/gbrowse2/languages/it.pm
/etc/gbrowse2/languages/ja.pm
/etc/gbrowse2/languages/ko.pm
/etc/gbrowse2/languages/nl.pm
/etc/gbrowse2/languages/pl.pm
/etc/gbrowse2/languages/ru.pm
/etc/gbrowse2/languages/zh.pm
/etc/gbrowse2/languages/zh_cn.pm
/etc/gbrowse2/plugins/AlignTwoSequences.pm
/etc/gbrowse2/plugins/Aligner.pm
/etc/gbrowse2/plugins/AttributeHiliter.pm
/etc/gbrowse2/plugins/BatchDumper.pm
/etc/gbrowse2/plugins/Blat.pm
/etc/gbrowse2/plugins/CMapDumper.pm
/etc/gbrowse2/plugins/CreateBlastDB.pm
/etc/gbrowse2/plugins/FBTableDumper.pm
/etc/gbrowse2/plugins/FastaDumper.pm
/etc/gbrowse2/plugins/FilterTest.pm
/etc/gbrowse2/plugins/GeneFinder.pm
/etc/gbrowse2/plugins/LDAPAuthenticate.pm
/etc/gbrowse2/plugins/OligoFinder.pm
/etc/gbrowse2/plugins/PamAuthenticate.pm
/etc/gbrowse2/plugins/PrimerDesigner.pm
/etc/gbrowse2/plugins/ProteinDumper.pm
/etc/gbrowse2/plugins/RandomGene.pm
/etc/gbrowse2/plugins/RestrictionAnnotator.pm
/etc/gbrowse2/plugins/SequenceDumper.pm
/etc/gbrowse2/plugins/SimpleTrackFinder.pm
/etc/gbrowse2/plugins/SinWave.pm
/etc/gbrowse2/plugins/SourceTrackFinder.pm
/etc/gbrowse2/plugins/Spectrogram.pm
/etc/gbrowse2/plugins/Submitter.pm
/etc/gbrowse2/plugins/TestAuthenticator.pm
/etc/gbrowse2/plugins/TestFinder.pm
/etc/gbrowse2/plugins/TrackDumper.pm
/etc/gbrowse2/plugins/TrackFinder.pm
/etc/gbrowse2/plugins/test.pm
/etc/gbrowse2/synteny/oryza.synconf.disabled
/etc/gbrowse2/synteny/rice_synteny.conf
/etc/gbrowse2/synteny/wild_rice_synteny.conf
/etc/gbrowse2/themes/solid_gray_colors
/etc/gbrowse2/themes/transparent_colors
/etc/gbrowse2/themes/warm_colors
/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-27jEyE/blib/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-EXfEDE/blib/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-EZitTT/blib/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-X2VOPv/blib/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-hEDg4u/blib/etc/httpd/conf.d/gbrowse2.conf
/root/.cpan/build/GBrowse-2.48-j8uGQI/blib/etc/httpd/conf.d/gbrowse2.conf
/var/lib/gbrowse2
/var/lib/gbrowse2/databases
/var/lib/gbrowse2/sessions
/var/lib/gbrowse2/userdata
/var/lib/gbrowse2/databases/admin_uploads
/var/lib/gbrowse2/databases/gbrowse_syn
/var/lib/gbrowse2/databases/ideograms
/var/lib/gbrowse2/databases/pop_demo
/var/lib/gbrowse2/databases/yeast_chr1+2
/var/lib/gbrowse2/databases/yeast_scaffolds
/var/lib/gbrowse2/databases/admin_uploads/README
/var/lib/gbrowse2/databases/gbrowse_syn/alignments
/var/lib/gbrowse2/databases/gbrowse_syn/rice
/var/lib/gbrowse2/databases/gbrowse_syn/wild_rice
/var/lib/gbrowse2/databases/gbrowse_syn/alignments/rice.aln.gz
/var/lib/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
/var/lib/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
/var/lib/gbrowse2/databases/ideograms/human_cytobands.gff
/var/lib/gbrowse2/databases/ideograms/mouse_cytobands.gff
/var/lib/gbrowse2/databases/ideograms/rat_cytobands.gff
/var/lib/gbrowse2/databases/pop_demo/pop_demo.gff3
/var/lib/gbrowse2/databases/yeast_chr1+2/yeast_chr1+2.gff3
/var/lib/gbrowse2/databases/yeast_scaffolds/chr1.fa
/var/lib/gbrowse2/databases/yeast_scaffolds/chr2.fa
/var/lib/gbrowse2/databases/yeast_scaffolds/chromosomes.gff3



On Wed, Mar 28, 2012 at 5:38 PM, Scott Cain <[hidden email]> wrote:
Omar,

Are you familiar with the locate command?  Run updatedb and then try

 locate gbrowse2

to see where it went.

Scott


On Wed, Mar 28, 2012 at 5:23 PM, Omar Darwish <[hidden email]> wrote:
> Oh No it is empty!
>
>
> On Wed, Mar 28, 2012 at 5:22 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Omar,
>>
>> Is the gbrowse2 directory in /var/www/html?
>>
>> Scott
>>
>> (please leave the GBrowse list cc'ed so the debugging can be archived)
>>
>>
>> On Wed, Mar 28, 2012 at 5:21 PM, Omar Darwish <[hidden email]>
>> wrote:
>> > Yes, /var/www exists and it has (html, error, cgi-bin and icons)
>> >
>> >
>> > On Wed, Mar 28, 2012 at 5:11 PM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Omar,
>> >>
>> >> Well then I guessed wrong what the problem was.  Does /var/www exist?
>> >> Does it have an html directory, and a gbrowse2 directory in it?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Mar 28, 2012 at 5:07 PM, Omar Darwish <[hidden email]>
>> >> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > I could not find this directory /usr/local/apache ?? i can only see
>> >> > is
>> >> > this
>> >> > one /etc/httpd
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Mar 28, 2012 at 4:48 PM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi Omar,
>> >> >>
>> >> >> I just looked back at the installation log that you sent--the
>> >> >> installer suggested that you install in /usr/local/apache, which is
>> >> >> where it would be if you built apache from source, which I'm
>> >> >> guessing
>> >> >> you didn't do.  The easiest way to fix that is to "rm -rf
>> >> >> /usr/local/apache" and force the installation of GBrowse again:
>> >> >>
>> >> >>  sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'
>> >> >>
>> >> >> The reason that happened is you tried to install GBrowse before you
>> >> >> installed apache, and when the installer didn't find the directories
>> >> >> for the system installed apache, it assumed you must have one you
>> >> >> installed yourself, and created /usr/local/apache and put the
>> >> >> GBrowse
>> >> >> files there.  (A possible second explanation is that CentOS changed
>> >> >> where it's apache directories are, but I don't think that is it
>> >> >> since
>> >> >> I probably would have heard about it by now.)
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Mar 28, 2012 at 4:26 PM, Omar Darwish <[hidden email]>
>> >> >> wrote:
>> >> >> > Thanks Scott, I guess it worked After installing perl DBI!!
>> >> >> > To double check, i tried executing ( sudo perl -MCPAN -e 'install
>> >> >> > Bio::Graphics::Browser2' ) one more time, it returned the lines
>> >> >> > below:
>> >> >> > CPAN: Storable loaded ok (v2.20)
>> >> >> > Going to read '/root/.cpan/Metadata'
>> >> >> >   Database was generated on Wed, 28 Mar 2012 16:10:31 GMT
>> >> >> > Bio::Graphics::Browser2 is up to date (2.48).
>> >> >> >
>> >> >> >
>> >> >> > Apache server is running, I tried to access
>> >> >> > (http://localhost/gbrowse2)
>> >> >> > I
>> >> >> > got page Not Found
>> >> >> > Do I need to do any kind of configuration ?
>> >> >> >
>> >> >> > Regards
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Mar 28, 2012 at 4:11 PM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Hi Omar,
>> >> >> >>
>> >> >> >> While you shouldn't need (and didn't used to need) the perl
>> >> >> >> module
>> >> >> >> DBI
>> >> >> >> to install GBrowse, apparently something has changed recently.
>> >> >> >>  If
>> >> >> >> you
>> >> >> >> install perl-DBI with yum things should work.  In reality, unless
>> >> >> >> you
>> >> >> >> are just installing GBrowse to do the tutorial and nothing else,
>> >> >> >> you're going to want DBI anyway.
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Mar 28, 2012 at 4:03 PM, Omar Darwish
>> >> >> >> <[hidden email]>
>> >> >> >> wrote:
>> >> >> >> > Hi Scott,
>> >> >> >> >
>> >> >> >> > I installed the Bio::Graphics, it went fine i guess, please
>> >> >> >> > take a
>> >> >> >> > look
>> >> >> >> > at
>> >> >> >> > the new attached output file
>> >> >> >> >
>> >> >> >> > Thanks
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Mar 28, 2012 at 3:51 PM, Scott Cain
>> >> >> >> > <[hidden email]>
>> >> >> >> > wrote:
>> >> >> >> >>
>> >> >> >> >> Hi Omar,
>> >> >> >> >>
>> >> >> >> >> Bio::Graphics isn't getting installed since GD won't install.
>> >> >> >> >>  GD
>> >> >> >> >> won't install because you don't have the libgd headers
>> >> >> >> >> installed.
>> >> >> >> >>  The
>> >> >> >> >> easiest thing to do would be to use yum to install GD:
>> >> >> >> >>
>> >> >> >> >>  sudo yum install perl-GD
>> >> >> >> >>
>> >> >> >> >> but to do that you might have to add rpmforge as a yum
>> >> >> >> >> repository.
>> >> >> >> >>  See:
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>  http://wiki.centos.org/AdditionalResources/Repositories/RPMForge
>> >> >> >> >>
>> >> >> >> >> Scott
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, Mar 28, 2012 at 3:30 PM, Omar Darwish
>> >> >> >> >> <[hidden email]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Hi Scott,
>> >> >> >> >> > Please see the attached file
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Wed, Mar 28, 2012 at 3:14 PM, Scott Cain
>> >> >> >> >> > <[hidden email]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >>
>> >> >> >> >> >> Yes, if you type "script" before entering the cpan shell,
>> >> >> >> >> >> everything
>> >> >> >> >> >> you type and the responses on the screen are saved to a
>> >> >> >> >> >> file.
>> >> >> >> >> >>  To
>> >> >> >> >> >> make
>> >> >> >> >> >> script quit, you type control-D.
>> >> >> >> >> >>
>> >> >> >> >> >> Scott
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Wed, Mar 28, 2012 at 3:07 PM, Omar Darwish
>> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >> > Oh, I am not really sure about your question, Is there
>> >> >> >> >> >> > any
>> >> >> >> >> >> > way
>> >> >> >> >> >> > (command)
>> >> >> >> >> >> > i
>> >> >> >> >> >> > can save the installation output to a file so that i can
>> >> >> >> >> >> > send
>> >> >> >> >> >> > it
>> >> >> >> >> >> > to
>> >> >> >> >> >> > you
>> >> >> >> >> >> > ?
>> >> >> >> >> >> >
>> >> >> >> >> >> > Thanks
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > On Wed, Mar 28, 2012 at 3:03 PM, Scott Cain
>> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> That is a pretty massive failure--it looks like all of
>> >> >> >> >> >> >> the
>> >> >> >> >> >> >> tests
>> >> >> >> >> >> >> failed to even run.  Did the prerequisites installed
>> >> >> >> >> >> >> with
>> >> >> >> >> >> >> the
>> >> >> >> >> >> >> cpan
>> >> >> >> >> >> >> shell install properly?
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> Scott
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> On Wed, Mar 28, 2012 at 2:59 PM, Omar Darwish
>> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> > Below the last lines i got from the Installation
>> >> >> >> >> >> >> > process,
>> >> >> >> >> >> >> > I
>> >> >> >> >> >> >> > am
>> >> >> >> >> >> >> > not
>> >> >> >> >> >> >> > sure
>> >> >> >> >> >> >> > if
>> >> >> >> >> >> >> > they can help:
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > Test Summary Report
>> >> >> >> >> >> >> > -------------------
>> >> >> >> >> >> >> > t/00.compile.t          (Wstat: 4352 Tests: 77 Failed:
>> >> >> >> >> >> >> > 17)
>> >> >> >> >> >> >> >   Failed tests:  1, 3, 5, 7, 10, 12, 14, 16-17, 30,
>> >> >> >> >> >> >> > 32,
>> >> >> >> >> >> >> > 34
>> >> >> >> >> >> >> >                 36, 40, 42, 47, 76
>> >> >> >> >> >> >> >   Non-zero exit status: 17
>> >> >> >> >> >> >> > t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 90 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/03.render.t           (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> >> > t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 47 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: No plan found in TAP output
>> >> >> >> >> >> >> > t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 26 tests but
>> >> >> >> >> >> >> > ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed:
>> >> >> >> >> >> >> > 0)
>> >> >> >> >> >> >> >   Non-zero exit status: 2
>> >> >> >> >> >> >> >   Parse errors: Bad plan.  You planned 3 tests but ran
>> >> >> >> >> >> >> > 0.
>> >> >> >> >> >> >> > Files=9, Tests=90,  2 wallclock secs ( 0.04 usr  0.02
>> >> >> >> >> >> >> > sys
>> >> >> >> >> >> >> > +
>> >> >> >> >> >> >> >  1.97
>> >> >> >> >> >> >> > cusr
>> >> >> >> >> >> >> >  0.25
>> >> >> >> >> >> >> > csys =  2.28 CPU)
>> >> >> >> >> >> >> > Result: FAIL
>> >> >> >> >> >> >> > Failed 7/9 test programs. 17/90 subtests failed.
>> >> >> >> >> >> >> >   LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> >> >   ./Build test -- NOT OK
>> >> >> >> >> >> >> > //hint// to see the cpan-testers results for
>> >> >> >> >> >> >> > installing
>> >> >> >> >> >> >> > this
>> >> >> >> >> >> >> > module,
>> >> >> >> >> >> >> > try:
>> >> >> >> >> >> >> >   reports LDS/GBrowse-2.48.tar.gz
>> >> >> >> >> >> >> > Warning (usually harmless): 'YAML' not installed, will
>> >> >> >> >> >> >> > not
>> >> >> >> >> >> >> > store
>> >> >> >> >> >> >> > persistent
>> >> >> >> >> >> >> > state
>> >> >> >> >> >> >> > Running Build install
>> >> >> >> >> >> >> >   make test had returned bad status, won't install
>> >> >> >> >> >> >> > without
>> >> >> >> >> >> >> > force
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > On Wed, Mar 28, 2012 at 1:58 PM, Scott Cain
>> >> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> Hi Omar,
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> What sort of errors?  Do you have developers tools
>> >> >> >> >> >> >> >> like
>> >> >> >> >> >> >> >> make
>> >> >> >> >> >> >> >> and
>> >> >> >> >> >> >> >> gcc
>> >> >> >> >> >> >> >> installed?
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> Scott
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> PS: I took the gmane list out of the cc list and
>> >> >> >> >> >> >> >> added
>> >> >> >> >> >> >> >> GBrowse.
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> On Wed, Mar 28, 2012 at 1:37 PM, Omar Darwish
>> >> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> >> > Hi Scott,
>> >> >> >> >> >> >> >> > I tried this command,
>> >> >> >> >> >> >> >> > sudo perl -MCPAN -e 'install
>> >> >> >> >> >> >> >> > Bio::Graphics::Browser2'
>> >> >> >> >> >> >> >> > ...
>> >> >> >> >> >> >> >> > It
>> >> >> >> >> >> >> >> > worked
>> >> >> >> >> >> >> >> > on Ubuntu but returned errors on both Fedora &
>> >> >> >> >> >> >> >> > CentOS.
>> >> >> >> >> >> >> >> > What do you think?
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > Thanks,
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > On Tue, Mar 27, 2012 at 6:23 PM, Omar Darwish
>> >> >> >> >> >> >> >> > <[hidden email]>
>> >> >> >> >> >> >> >> > wrote:
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> Thanks Scott, I'll give it a try and get back to
>> >> >> >> >> >> >> >> >> you
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> On Tue, Mar 27, 2012 at 4:37 PM, Scott Cain
>> >> >> >> >> >> >> >> >> <[hidden email]>
>> >> >> >> >> >> >> >> >> wrote:
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> Hi Omar,
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> From source/the cpan shell since there aren't
>> >> >> >> >> >> >> >> >>> RPMs
>> >> >> >> >> >> >> >> >>> for
>> >> >> >> >> >> >> >> >>> GBrowse
>> >> >> >> >> >> >> >> >>> (though
>> >> >> >> >> >> >> >> >>> there is a debian package that works with debian
>> >> >> >> >> >> >> >> >>> and
>> >> >> >> >> >> >> >> >>> ubuntu).
>> >> >> >> >> >> >> >> >>>  Also,
>> >> >> >> >> >> >> >> >>> if you can turn off SELinux it makes life easier.
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> Scott
>> >> >> >> >> >> >> >> >>>
>> >> >> >> >> >> >> >> >>> On Tue, Mar 27, 2012 at 4:22 PM, Omar Darwish
>> >> >> >> >> >> >> >> >>> <[hidden email]>
>> >> >> >> >> >> >> >> >>> wrote:
>> >> >> >> >> >> >> >> >>> > Hello all,
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > What i the easiest way to install Gbrowse2 on
>> >> >> >> >> >> >> >> >>> > CentOS
>> >> >> >> >> >> >> >> >>> > &
>> >> >> >> >> >> >> >> >>> > Fedora
>> >> >> >> >> >> >> >> >>> > ??
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > --
>> >> >> >> >> >> >> >> >>> > Thank you,
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> >
>> >> >> >> >> >> >> >> >>> > ------------------------------------------------------------------------------
>> >> >> >> >> >> >> >> >>> > This SF email is sponsosred by:
>> >> >> >> >> >> >> >> >>> > Try Windows Azure free for 90 days Click Here
>> >> >> >> >> >> >> >> >>> > http://p.sf.net/sfu/sfd2d-msazure
>> >> >> >> >> >> >> >> >>> > _______________________________________________
>> >> >> >> >> >> >> >> >>> > 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
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> --
>> >> >> >> >> >> >> >> >> Regards,
>> >> >> >> >> >> >> >> >> Omar
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >> > --
>> >> >> >> >> >> >> >> > Regards,
>> >> >> >> >> >> >> >> > Omar
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> --
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> >> >> 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
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >> > --
>> >> >> >> >> >> >> > Regards,
>> >> >> >> >> >> >> > Omar
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> --
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> >> 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
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > --
>> >> >> >> >> >> > Regards,
>> >> >> >> >> >> > Omar
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> >> 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
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Regards,
>> >> >> >> >> > Omar
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> ------------------------------------------------------------------------
>> >> >> >> >> 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
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Regards,
>> >> >> >> > Omar
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> 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
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Regards,
>> >> >> > Omar
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> 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
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > Omar
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> 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
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Omar
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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
>
>
>
>
> --
> Regards,
> Omar



--
------------------------------------------------------------------------
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



--
Regards,
Omar

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