Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

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Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Chandan Kumar Singh
Hi

Installing user home specific Gbrowse instance is not very easy as of
now. I am still struggling at a stage where apache access to user-home
directories are denied.

I did not install Apache to user home as the idea was not very
pleasing to me and there is already a root installation of Apache
listening on port 80. I understand that the root Apache can reverse
proxy requests to user specific instance of Apache running on some
other port@localhost.

But instead of Apache in user home, I will rather have a light weight
http server preferably something more perlish (like Starman or other
PSGI compliant servers) so that user specific Gbrowse installation is
smoother and void of permission issues even if limited in performance
to begin with.

I request opinion on this issue especially if the idea is worth
pondering about and if it is a task requiring moderate effort.

Thanks
Chandan

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computing security and archiving is rapidly being adopted across the IT
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Todd Harris
It's entirely possible to run GBrowse under a PSGI/Plack stack.  It's a thing of beauty to not have to fuss with Apache.

However, some changes must be made to several core GBrowse files to get this to work.  As I recall, there are several places where GBrowse issues redirects that fall over under a Plack stack.

I have a fork of GBrowse where I'm putting my work on this.  Once I think it's ready and not likely to break GBrowse proper, I'll send a pull request to the maintainers.  Drop me a line if you'd like to help with this.

Todd


On Sep 9, 2011, at 4:02 AM, Chandan Kumar Singh wrote:

> Hi
>
> Installing user home specific Gbrowse instance is not very easy as of
> now. I am still struggling at a stage where apache access to user-home
> directories are denied.
>
> I did not install Apache to user home as the idea was not very
> pleasing to me and there is already a root installation of Apache
> listening on port 80. I understand that the root Apache can reverse
> proxy requests to user specific instance of Apache running on some
> other port@localhost.
>
> But instead of Apache in user home, I will rather have a light weight
> http server preferably something more perlish (like Starman or other
> PSGI compliant servers) so that user specific Gbrowse installation is
> smoother and void of permission issues even if limited in performance
> to begin with.
>
> I request opinion on this issue especially if the idea is worth
> pondering about and if it is a task requiring moderate effort.
>
> Thanks
> Chandan
>
> ------------------------------------------------------------------------------
> Why Cloud-Based Security and Archiving Make Sense
> Osterman Research conducted this study that outlines how and why cloud
> computing security and archiving is rapidly being adopted across the IT
> space for its ease of implementation, lower cost, and increased
> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Chandan Kumar Singh
Hi Todd

I am in awe of Plack stack after Catalyst 5.9 and like to use more of
it without bothering the root web server much. It was in this
hindsight that I wanted a gbrowse instance to be more integrated to a
catalyst based web app under development.

I will love to help you in this effort.

Thanks
Chandan



On Fri, Sep 9, 2011 at 3:39 PM, Todd Harris <[hidden email]> wrote:

> It's entirely possible to run GBrowse under a PSGI/Plack stack.  It's a thing of beauty to not have to fuss with Apache.
>
> However, some changes must be made to several core GBrowse files to get this to work.  As I recall, there are several places where GBrowse issues redirects that fall over under a Plack stack.
>
> I have a fork of GBrowse where I'm putting my work on this.  Once I think it's ready and not likely to break GBrowse proper, I'll send a pull request to the maintainers.  Drop me a line if you'd like to help with this.
>
> Todd
>
>
> On Sep 9, 2011, at 4:02 AM, Chandan Kumar Singh wrote:
>
>> Hi
>>
>> Installing user home specific Gbrowse instance is not very easy as of
>> now. I am still struggling at a stage where apache access to user-home
>> directories are denied.
>>
>> I did not install Apache to user home as the idea was not very
>> pleasing to me and there is already a root installation of Apache
>> listening on port 80. I understand that the root Apache can reverse
>> proxy requests to user specific instance of Apache running on some
>> other port@localhost.
>>
>> But instead of Apache in user home, I will rather have a light weight
>> http server preferably something more perlish (like Starman or other
>> PSGI compliant servers) so that user specific Gbrowse installation is
>> smoother and void of permission issues even if limited in performance
>> to begin with.
>>
>> I request opinion on this issue especially if the idea is worth
>> pondering about and if it is a task requiring moderate effort.
>>
>> Thanks
>> Chandan
>>
>> ------------------------------------------------------------------------------
>> Why Cloud-Based Security and Archiving Make Sense
>> Osterman Research conducted this study that outlines how and why cloud
>> computing security and archiving is rapidly being adopted across the IT
>> space for its ease of implementation, lower cost, and increased
>> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Todd Harris
Hi Chandan -

Im traveling at the moment.  I will prepare some docs in the next day or so and send your way.

Todd




On Sep 9, 2011, at 12:20 PM, Chandan Kumar Singh wrote:

> Hi Todd
>
> I am in awe of Plack stack after Catalyst 5.9 and like to use more of
> it without bothering the root web server much. It was in this
> hindsight that I wanted a gbrowse instance to be more integrated to a
> catalyst based web app under development.
>
> I will love to help you in this effort.
>
> Thanks
> Chandan
>
>
>
> On Fri, Sep 9, 2011 at 3:39 PM, Todd Harris <[hidden email]> wrote:
>> It's entirely possible to run GBrowse under a PSGI/Plack stack.  It's a thing of beauty to not have to fuss with Apache.
>>
>> However, some changes must be made to several core GBrowse files to get this to work.  As I recall, there are several places where GBrowse issues redirects that fall over under a Plack stack.
>>
>> I have a fork of GBrowse where I'm putting my work on this.  Once I think it's ready and not likely to break GBrowse proper, I'll send a pull request to the maintainers.  Drop me a line if you'd like to help with this.
>>
>> Todd
>>
>>
>> On Sep 9, 2011, at 4:02 AM, Chandan Kumar Singh wrote:
>>
>>> Hi
>>>
>>> Installing user home specific Gbrowse instance is not very easy as of
>>> now. I am still struggling at a stage where apache access to user-home
>>> directories are denied.
>>>
>>> I did not install Apache to user home as the idea was not very
>>> pleasing to me and there is already a root installation of Apache
>>> listening on port 80. I understand that the root Apache can reverse
>>> proxy requests to user specific instance of Apache running on some
>>> other port@localhost.
>>>
>>> But instead of Apache in user home, I will rather have a light weight
>>> http server preferably something more perlish (like Starman or other
>>> PSGI compliant servers) so that user specific Gbrowse installation is
>>> smoother and void of permission issues even if limited in performance
>>> to begin with.
>>>
>>> I request opinion on this issue especially if the idea is worth
>>> pondering about and if it is a task requiring moderate effort.
>>>
>>> Thanks
>>> Chandan
>>>
>>> ------------------------------------------------------------------------------
>>> Why Cloud-Based Security and Archiving Make Sense
>>> Osterman Research conducted this study that outlines how and why cloud
>>> computing security and archiving is rapidly being adopted across the IT
>>> space for its ease of implementation, lower cost, and increased
>>> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>


------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Fields, Christopher J
Todd,

Is this fork on github or just local?  

chris

On Sep 9, 2011, at 5:42 AM, Todd Harris wrote:

> Hi Chandan -
>
> Im traveling at the moment.  I will prepare some docs in the next day or so and send your way.
>
> Todd
>
>
>
>
> On Sep 9, 2011, at 12:20 PM, Chandan Kumar Singh wrote:
>
>> Hi Todd
>>
>> I am in awe of Plack stack after Catalyst 5.9 and like to use more of
>> it without bothering the root web server much. It was in this
>> hindsight that I wanted a gbrowse instance to be more integrated to a
>> catalyst based web app under development.
>>
>> I will love to help you in this effort.
>>
>> Thanks
>> Chandan
>>
>>
>>
>> On Fri, Sep 9, 2011 at 3:39 PM, Todd Harris <[hidden email]> wrote:
>>> It's entirely possible to run GBrowse under a PSGI/Plack stack.  It's a thing of beauty to not have to fuss with Apache.
>>>
>>> However, some changes must be made to several core GBrowse files to get this to work.  As I recall, there are several places where GBrowse issues redirects that fall over under a Plack stack.
>>>
>>> I have a fork of GBrowse where I'm putting my work on this.  Once I think it's ready and not likely to break GBrowse proper, I'll send a pull request to the maintainers.  Drop me a line if you'd like to help with this.
>>>
>>> Todd
>>>
>>>
>>> On Sep 9, 2011, at 4:02 AM, Chandan Kumar Singh wrote:
>>>
>>>> Hi
>>>>
>>>> Installing user home specific Gbrowse instance is not very easy as of
>>>> now. I am still struggling at a stage where apache access to user-home
>>>> directories are denied.
>>>>
>>>> I did not install Apache to user home as the idea was not very
>>>> pleasing to me and there is already a root installation of Apache
>>>> listening on port 80. I understand that the root Apache can reverse
>>>> proxy requests to user specific instance of Apache running on some
>>>> other port@localhost.
>>>>
>>>> But instead of Apache in user home, I will rather have a light weight
>>>> http server preferably something more perlish (like Starman or other
>>>> PSGI compliant servers) so that user specific Gbrowse installation is
>>>> smoother and void of permission issues even if limited in performance
>>>> to begin with.
>>>>
>>>> I request opinion on this issue especially if the idea is worth
>>>> pondering about and if it is a task requiring moderate effort.
>>>>
>>>> Thanks
>>>> Chandan
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Why Cloud-Based Security and Archiving Make Sense
>>>> Osterman Research conducted this study that outlines how and why cloud
>>>> computing security and archiving is rapidly being adopted across the IT
>>>> space for its ease of implementation, lower cost, and increased
>>>> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>
>
> ------------------------------------------------------------------------------
> Why Cloud-Based Security and Archiving Make Sense
> Osterman Research conducted this study that outlines how and why cloud
> computing security and archiving is rapidly being adopted across the IT
> space for its ease of implementation, lower cost, and increased
> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Kent source for Bio::DB::BigFile

Miquel Ràmia
Hi,

Hi, I'm trying to compile Bio::DB::BigFile. I've followed the
instructions in Kent README to compile Kent source, bigWig.h is in
src/inc/ and jkweb.a in src/lib/x86_64/ (I manually set MACHTYPE to
x86_64), but i get the error:

"Please enter the location of Kent source tree: ~/kent/src/
Can't find the bigWig.h and jkweb.a files at this location."

In this old thread I've read that I should compile Kent source with
'sudo', which I didn't
(http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/6954), but
when I do, jkweb.a is not created. In the thread it's suggested that the
modified MACHTYPE is lost when 'sudo' is used, but I do 'sudo echo
$MACHTYPE' and is correctly set.

What should I check?

cheers!



--
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)



------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Kent source for Bio::DB::BigFile

Chandan Kumar Singh
HI

Enter the full path without the '~' . Even $HOME might work but it is
so easy to give the full path itself.

Thanks
Chandan


2011/9/9 Miquel Ràmia <[hidden email]>:

> Hi,
>
> Hi, I'm trying to compile Bio::DB::BigFile. I've followed the
> instructions in Kent README to compile Kent source, bigWig.h is in
> src/inc/ and jkweb.a in src/lib/x86_64/ (I manually set MACHTYPE to
> x86_64), but i get the error:
>
> "Please enter the location of Kent source tree: ~/kent/src/
> Can't find the bigWig.h and jkweb.a files at this location."
>
> In this old thread I've read that I should compile Kent source with
> 'sudo', which I didn't
> (http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/6954), but
> when I do, jkweb.a is not created. In the thread it's suggested that the
> modified MACHTYPE is lost when 'sudo' is used, but I do 'sudo echo
> $MACHTYPE' and is correctly set.
>
> What should I check?
>
> cheers!
>
>
>
> --
> Miquel Ràmia Jesús
> PhD. student (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Autònoma de Barcelona (UAB)
> 08193, Cerdanyola del Vallès
> Barcelona (Spain)
>
>
>
> ------------------------------------------------------------------------------
> Why Cloud-Based Security and Archiving Make Sense
> Osterman Research conducted this study that outlines how and why cloud
> computing security and archiving is rapidly being adopted across the IT
> space for its ease of implementation, lower cost, and increased
> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Robert Buels
In reply to this post by Fields, Christopher J
On 09/09/2011 05:55 AM, Fields, Christopher J wrote:
> Is this fork on github or just local?

Yeah, I'm interested in keeping my eye on that too.


------------------------------------------------------------------------------
Why Cloud-Based Security and Archiving Make Sense
Osterman Research conducted this study that outlines how and why cloud
computing security and archiving is rapidly being adopted across the IT
space for its ease of implementation, lower cost, and increased
reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Todd Harris
Chris, Robert, Chandan --

Here's some documentation about my little PSGI wrapper around the GBrowse CGIs.  

http://toddharris.net/blog/2011/09/11/running-the-generic-genome-browser-under-psgiplack/

And the fork:

http://github.com/tharris/GBrowse-PSGI

GBrowse is pretty tightly tied not to Apache (I actually run it under nginx) but to CGI.  I believe we could refactor it fairly easily using something like CGI::Emulate::PSGI as a starting point.  A more complete re-factor could be a substantive amount of work and significant departure from the current codebase.  I've started this on a clone to do some local experimentation.

Todd


On Sep 9, 2011, at 9:22 PM, Robert Buels wrote:

> On 09/09/2011 05:55 AM, Fields, Christopher J wrote:
>> Is this fork on github or just local?
>
> Yeah, I'm interested in keeping my eye on that too.
>
>
> ------------------------------------------------------------------------------
> Why Cloud-Based Security and Archiving Make Sense
> Osterman Research conducted this study that outlines how and why cloud
> computing security and archiving is rapidly being adopted across the IT
> space for its ease of implementation, lower cost, and increased
> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops?   How do next-generation virtual desktops
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Re: Kent source for Bio::DB::BigFile

Miquel Ràmia
In reply to this post by Chandan Kumar Singh
Hi again,

Sorry, I only used the '~' in the message, I actually used the full path
each time I tried.

Tried as root exporting MACHTYPE and using 'make CXXFLAGS=-fPIC
CFLAGS=-fPIC CPPFLAGS=-fPIC' as suggested, jkweb.a was created
correctly, but compiling BigFile still says that 'Can't find the
bigWig.h and jkweb.a files at this location'.


On 09/09/2011 05:26 PM, Chandan Kumar Singh wrote:

> HI
>
> Enter the full path without the '~' . Even $HOME might work but it is
> so easy to give the full path itself.
>
> Thanks
> Chandan
>
>
>

--
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)



------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops?   How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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Re: Kent source for Bio::DB::BigFile

Bremen Braun
I solved this problem last time I tried by moving the jkweb.a from my kent/src/lib/$MACHTYPE to kent/src/lib

2011/9/12 Miquel Ràmia <[hidden email]>
Hi again,

Sorry, I only used the '~' in the message, I actually used the full path
each time I tried.

Tried as root exporting MACHTYPE and using 'make CXXFLAGS=-fPIC
CFLAGS=-fPIC CPPFLAGS=-fPIC' as suggested, jkweb.a was created
correctly, but compiling BigFile still says that 'Can't find the
bigWig.h and jkweb.a files at this location'.


On 09/09/2011 05:26 PM, Chandan Kumar Singh wrote:
> HI
>
> Enter the full path without the '~' . Even $HOME might work but it is
> so easy to give the full path itself.
>
> Thanks
> Chandan
>
>
>

--
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)



------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops?   How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
_______________________________________________
Gmod-gbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Bremen Braun
IT Specialist
USDA-ARS


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Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops?   How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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Re: Why is Gbrowse so tied to Apache ? Will an alternative be easier to implement?

Robert Buels
In reply to this post by Todd Harris
On 09/12/2011 12:43 AM, Todd Harris wrote:
> GBrowse is pretty tightly tied not to Apache (I actually run it under nginx) but to CGI.  I believe we could refactor it fairly easily using something like CGI::Emulate::PSGI as a starting point.  A more complete re-factor could be a substantive amount of work and significant departure from the current codebase.  I've started this on a clone to do some local experimentation.

Yes, probably either CGI::Emulate::PSGI or CGI::PSGI would make sense,
in the short term.

Rob

------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops?   How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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Re: Kent source for Bio::DB::BigFile

Miquel Ràmia
In reply to this post by Bremen Braun
Hi all,

I've managed to compile kent source and do the bigFile ./build
correctly, but './build test' gives me these errors:

t/01.bigwig.t ....... Can't load
'/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile: /home/mike/.cpan/build/Bio-
BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: euncompress at /usr/lib/perl/5.10/DynaLoader.pm line 193.
  at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests
t/02.bigbed.t ....... Can't load
'/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile: /home/mike/.cpan/build/Bio-
BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: euncompress at /usr/lib/perl/5.10/DynaLoader.pm line 193.
  at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/03.bigwig_high.t .. Can't load
'/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile: /home/mike/.cpan/build/Bio-
BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: euncompress at /usr/lib/perl/5.10/DynaLoader.pm line 193.
  at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests
t/04.bigbed_high.t .. Can't load
'/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: euncompress at /usr/lib/perl/5.10/DynaLoader.pm line 193.
  at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigBed.pm
line 7.
BEGIN failed--compilation aborted at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigBed.pm
line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests
t/05.bigwig_set.t ... Can't load
'/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: euncompress at /usr/lib/perl/5.10/DynaLoader.pm line 193.
  at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWigSet.pm
line 177.
BEGIN failed--compilation aborted at
/home/mike/.cpan/build/Bio-BigFile-1.06-mVxySE/t/../lib/Bio/DB/BigWigSet.pm
line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
   Non-zero exit status: 2
   Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
   Non-zero exit status: 2
   Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
   Non-zero exit status: 2
   Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
   Non-zero exit status: 2
   Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
   Non-zero exit status: 2
   Parse errors: No plan found in TAP output
Files=5, Tests=0,  0 wallclock secs ( 0.02 usr  0.02 sys +  0.71 cusr  
0.10 csys =  0.85 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.


I don't have any clue on what to do, any suggestion?
Thanks!



--
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)



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