Re: pysam package

[Dominique Belhachemi <domibel@debian.org>]

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