[Biopython-dev] BioPython Debian packages uploaded (Was: BWA command line change?)

[Saket Choudhary]

Thanks Andreas,

Just for the record, I have now submitted this as a pull request:
https://github.com/biopython/biopython/pull/315

Saket

On 29 April 2014 14:43, Andreas Tille <andreas at an3as.eu> wrote:
> Hi,
>
> I have included the patch below in the just uploaded BioPython package.
> The package will need to passe the new queue due to the new packages for
> Python 3.3 and 3.4 so it might need some days to become available in
> Debian unstable.
>
> Besides the Python 3 support the other major change is that we try to
> run as many tests of the test suite as possible at package build time
> and there is also an autopkgtest added which means that in a regular
> basis the package is installed automatically on a clean system and the
> test suite is runned on the installation.
>
> As an additional hint for you as developers:  Here you can find all
> patches applied to the package:
>
>    http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/debian/patches/
>
> I think the only patch which I did not reported is
> biopython-from-pil-import-image.patch which I'd recommend to apply
> upstream as well (description is included).
>
> Kind regards and thanks for providing BioPython as free software
>
>      Andreas.
>
> On Tue, Apr 29, 2014 at 02:47:35AM +0530, Saket Choudhary wrote:
>> Commited a fix here:
>> https://github.com/saketkc/biopython/commit/d884ee6e12a798b974b3a3996e22b5292ab79be6
>>
>> If it looks good, I can send a PR?
>> Unfortunately my commit history is a bit muddled up on master.
>>
>> On 29 April 2014 01:53, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> > On Mon, Apr 28, 2014 at 9:07 PM, Saket Choudhary <saketkc at gmail.com> wrote:
>> >> This is turning out to be an issue with this particular version of
>> >> bwa[0.7.6a-r433];l
>> >> $ bwa7.6a aln
>> >> [main] unrecognized command 'aln'
>> >>
>> >> However the later two versions do support it, and the tests do pass:
>> >
>> > The simplest solution may be to check for that error during
>> > the header where we see if bwa is installed, and if it is
>> > missing the aln command skip the tests?
>> >
>> > Peter
>>
>
> --
> http://fam-tille.de