Bio::DB::BigFile and Bio::DB::Sam

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Bio::DB::BigFile and Bio::DB::Sam

Benjamin Hitz

The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?

Ben


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Saccharomyces Genome Project
Stanford University
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Re: Bio::DB::BigFile and Bio::DB::Sam

Scott Cain
Hi Ben,

Bio-BigFile does depend on Jim's code, so it won't work without it.
Bio-SamTools doesn't not depend on Jim's code, rather it depends on
Heng Li's SAMtools, and it won't work without it.

Scott


On Fri, May 13, 2011 at 2:54 PM, Benjamin Hitz <[hidden email]> wrote:

>
> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>
> Ben
>
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> [hidden email]
>
>
>
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Bio::DB::BigFile and Bio::DB::Sam

Fields, Christopher J
In reply to this post by Benjamin Hitz
Ben,

I think 'force install' is generally used to override instances where tests may fail but the modules compile fine with the perl interpreter (pure perl modules or ones where the linked C code/libraries are present and the XS glue code compiles successfully).  DBD::mysql, for instance, compiles fine on when installing from CPAN, but the tests may fail if db perms aren't set up properly; I could force install that as long as the compilation step proceeds.

In your case the required C libraries aren't even present, so I would assume they wouldn't install even with 'force install' as the build process wouldn't get past compilation.

In any case, I don't think either Bio::DB::BigFile or Bio::DB::Sam is absolutely required for GBrowse 2.

chris

On May 13, 2011, at 1:54 PM, Benjamin Hitz wrote:

>
> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>
> Ben
>
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> [hidden email]
>
>
>
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christopher Fields
Senior Research Scientist
National Center for Supercomputing Applications
Institute for Genomic Biology
University of Illinois Urbana-Champaign
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801


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Re: Bio::DB::BigFile and Bio::DB::Sam

Benjamin Hitz
>
> In your case the required C libraries aren't even present, so I would assume they wouldn't install even with 'force install' as the build process wouldn't get past compilation.

It doesn't even get past perl Build.PL.  But even if it did, yes, it wouldn't compile.
>
> In any case, I don't think either Bio::DB::BigFile or Bio::DB::Sam is absolutely required for GBrowse 2.

But they are absolutely required for me!  Ironically - I am 80% certain I am using Bio::DB::BigFile in Gbrowse without jim kent's source code installed.  At least, no one remembers installing it on that machine and we can't find it...

Ben

>
> chris
>
> On May 13, 2011, at 1:54 PM, Benjamin Hitz wrote:
>
>>
>> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
>> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>>
>> Ben
>>
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
>> to help boost performance applications - inlcuding clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> Christopher Fields
> Senior Research Scientist
> National Center for Supercomputing Applications
> Institute for Genomic Biology
> University of Illinois Urbana-Champaign
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
>

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
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Re: Bio::DB::BigFile and Bio::DB::Sam

Lincoln Stein
To use Bio::DB::BigFile and Bio::DB::Sam, you need the Jim Kent and SamTools libraries and header files, respectively. There are no pure Perl libraries that replicate that functionality as of yet, nor is there likely to be.

Lincoln

On Fri, May 13, 2011 at 4:44 PM, Benjamin Hitz <[hidden email]> wrote:
>
> In your case the required C libraries aren't even present, so I would assume they wouldn't install even with 'force install' as the build process wouldn't get past compilation.

It doesn't even get past perl Build.PL.  But even if it did, yes, it wouldn't compile.
>
> In any case, I don't think either Bio::DB::BigFile or Bio::DB::Sam is absolutely required for GBrowse 2.

But they are absolutely required for me!  Ironically - I am 80% certain I am using Bio::DB::BigFile in Gbrowse without jim kent's source code installed.  At least, no one remembers installing it on that machine and we can't find it...

Ben
>
> chris
>
> On May 13, 2011, at 1:54 PM, Benjamin Hitz wrote:
>
>>
>> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
>> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>>
>> Ben
>>
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
>> to help boost performance applications - inlcuding clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> Christopher Fields
> Senior Research Scientist
> National Center for Supercomputing Applications
> Institute for Genomic Biology
> University of Illinois Urbana-Champaign
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
>

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
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--
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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Bio::DB::BigFile and Bio::DB::Sam

Benjamin Hitz
That does make some amount of sense.
I am thinking that someone built the perl XS modules linked to jkweb.a and bigWig.h and then tossed the files.  So the perl module still works even though jkweb.a is long gone...

Ben

On May 13, 2011, at 2:07 PM, Lincoln Stein wrote:

To use Bio::DB::BigFile and Bio::DB::Sam, you need the Jim Kent and SamTools libraries and header files, respectively. There are no pure Perl libraries that replicate that functionality as of yet, nor is there likely to be.

Lincoln

On Fri, May 13, 2011 at 4:44 PM, Benjamin Hitz <[hidden email]> wrote:
>
> In your case the required C libraries aren't even present, so I would assume they wouldn't install even with 'force install' as the build process wouldn't get past compilation.

It doesn't even get past perl Build.PL.  But even if it did, yes, it wouldn't compile.
>
> In any case, I don't think either Bio::DB::BigFile or Bio::DB::Sam is absolutely required for GBrowse 2.

But they are absolutely required for me!  Ironically - I am 80% certain I am using Bio::DB::BigFile in Gbrowse without jim kent's source code installed.  At least, no one remembers installing it on that machine and we can't find it...

Ben
>
> chris
>
> On May 13, 2011, at 1:54 PM, Benjamin Hitz wrote:
>
>>
>> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
>> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>>
>> Ben
>>
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
>> to help boost performance applications - inlcuding clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> Christopher Fields
> Senior Research Scientist
> National Center for Supercomputing Applications
> Institute for Genomic Biology
> University of Illinois Urbana-Champaign
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
>

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]




------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
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Re: Bio::DB::BigFile and Bio::DB::Sam

Lincoln Stein
Once the module is compiled, you don't need jkweb.a any longer.

Lincoln

On Fri, May 13, 2011 at 5:13 PM, Benjamin Hitz <[hidden email]> wrote:
That does make some amount of sense.
I am thinking that someone built the perl XS modules linked to jkweb.a and bigWig.h and then tossed the files.  So the perl module still works even though jkweb.a is long gone...

Ben

On May 13, 2011, at 2:07 PM, Lincoln Stein wrote:

To use Bio::DB::BigFile and Bio::DB::Sam, you need the Jim Kent and SamTools libraries and header files, respectively. There are no pure Perl libraries that replicate that functionality as of yet, nor is there likely to be.

Lincoln

On Fri, May 13, 2011 at 4:44 PM, Benjamin Hitz <[hidden email]> wrote:
>
> In your case the required C libraries aren't even present, so I would assume they wouldn't install even with 'force install' as the build process wouldn't get past compilation.

It doesn't even get past perl Build.PL.  But even if it did, yes, it wouldn't compile.
>
> In any case, I don't think either Bio::DB::BigFile or Bio::DB::Sam is absolutely required for GBrowse 2.

But they are absolutely required for me!  Ironically - I am 80% certain I am using Bio::DB::BigFile in Gbrowse without jim kent's source code installed.  At least, no one remembers installing it on that machine and we can't find it...

Ben
>
> chris
>
> On May 13, 2011, at 1:54 PM, Benjamin Hitz wrote:
>
>>
>> The packages that hold these files (Bio::DB::BigFile and Bio::DB::Sam) - Bio-BigFile and Bio-SamTools have a "build" dependency on jim kent's C code.
>> Is this dependency strict from Gbrowse's perspective?  I.e,. if I force install or manually install native perl modules (without installing jkent) will it not work with Gbrowse 2?
>>
>> Ben
>>
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
>> to help boost performance applications - inlcuding clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> Christopher Fields
> Senior Research Scientist
> National Center for Supercomputing Applications
> Institute for Genomic Biology
> University of Illinois Urbana-Champaign
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
>

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

--
Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]






--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse