Bio-Samtools question

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Bio-Samtools question

Fields, Christopher J
Hi all,

I’ve started working on a side project that implements low-level bindings to htslib and it’s kin (including samtools and bcftools).  Part of this is to specifically target and optimize higher-level code (particularly bioperl bindings) w/o being reliant on having any of those bindings directly installed.

However, I found that recent changes in samtools by Sanger appear to require a pre-compiled shared libhts as well as libbam.  What I am thinking of doing is basically rewriting these to target specific versions of hts/samtools/bcftools, possibly bundling them together in downstream distributions (they’re really not large, particularly when compared to the current size of bioperl).  This can be done pretty easily via submodules; to see a stub example:

    https://github.com/HPCBio/HTSSam-XS

I think It also may be easier to not have these be part of the GBrowse-Adaptors code base, but be a separate ‘fork’ of the code.  e.g. I could fork the current code, remove non-samtools stuff, strip out the Bio-specific bindings (shouldn’t be hard), and then push up a new repo.  I could then add in support for htslib, newer samtools, etc.

Does that seem reasonable?  Or would it be simpler to copy over relevant files and start from scratch in a repo like the above?

chris
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Re: Bio-Samtools question

Fields, Christopher J
BTW, I’m at BOSC (and will be at CodeFest) in Boston should anyone be around :)

chris

On Jul 9, 2014, at 10:55 AM, Fields, Christopher J <[hidden email]> wrote:

> Hi all,
>
> I’ve started working on a side project that implements low-level bindings to htslib and it’s kin (including samtools and bcftools).  Part of this is to specifically target and optimize higher-level code (particularly bioperl bindings) w/o being reliant on having any of those bindings directly installed.
>
> However, I found that recent changes in samtools by Sanger appear to require a pre-compiled shared libhts as well as libbam.  What I am thinking of doing is basically rewriting these to target specific versions of hts/samtools/bcftools, possibly bundling them together in downstream distributions (they’re really not large, particularly when compared to the current size of bioperl).  This can be done pretty easily via submodules; to see a stub example:
>
>    https://github.com/HPCBio/HTSSam-XS
>
> I think It also may be easier to not have these be part of the GBrowse-Adaptors code base, but be a separate ‘fork’ of the code.  e.g. I could fork the current code, remove non-samtools stuff, strip out the Bio-specific bindings (shouldn’t be hard), and then push up a new repo.  I could then add in support for htslib, newer samtools, etc.
>
> Does that seem reasonable?  Or would it be simpler to copy over relevant files and start from scratch in a repo like the above?
>
> chris
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse