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Re: pysam package

I haven't been running pysam's tests, I just noticed while updating to 0.7 that there was a tests directory, and thought I should figure out how to run those.

Actually since you mentioned samtools. We've made a couple of modifications to the samtools package.

My coworker Henry Amrhein had a patch to return an error message instead of crashing when razip ran out of memory. Also I modified the samtools build scripts to build libbam as a shared library.


Fixing the oom segfault is at that git-repository in 'razip-oom-check'.

The modifications to the makefile were build-so. Along with corresponding debian package changes for the extra .deb. Though I'm probably not understanding how to name shared libraries properly as there was an error message about the soname.

Also the realization that I had a shared library for samtools, and the packaging team wanted a pysam without the embedded samtools source led me to try something I'll talk about in my next email.


On Wed, Dec 19, 2012 at 12:25:18PM -0500, Dominique Belhachemi wrote:
> Hi Diane,
> Running pysam tests during buildtime would be very helpful. I just run the
> tests manually and stumbled upon a bug in samtools.
> ( http://code.google.com/p/pysam/issues/detail?id=71 )  I wonder why this
> hasn't been fixed upstream, anyway, I am going to patch Debian's samtools
> package with the proposed fix.
> You can find Debian's pysam package here:
>    http://anonscm.debian.org/gitweb/?p=debian-med/pysam.git
> Howe are you running the tests right now? Is there a way to specify a
> temporary test output directory? This would be helpful in case we want to
> run the tests multiple times (python 2.6+2.7+3.0 etc..)
> Cheers
> -Dominique
> On Tue, Dec 18, 2012 at 10:02 PM, Diane Trout <diane@ghic.org> wrote:
> > Hi,
> >
> > I've been maintaining a pysam package for my lab, and realized that other
> > people might find pysam[1] useful.
> >
> > I used stdeb, git-buildpackage, and pbuilder to make my own package[2].
> > Unfortunately since I haven't actually talked to experienced packagers I'm
> > sure there are improvements I could be making. (For instance I need to
> > figure out how to run pysam's tests in debian/rules.)
> >
> > Would it be worthwhile to work toward making an official package? (And if
> > so a pointer for what to do next would be appreciated).
> >
> > Diane
> >
> > [1] https://code.google.com/p/pysam/
> > [2] http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=summary
> >

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