Re: BioPython Debian packages uploaded (Was: BWA command line change?)
Just for the record, I have now submitted this as a pull request:
On 29 April 2014 14:43, Andreas Tille <email@example.com> wrote:
> 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:
> 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
> On Tue, Apr 29, 2014 at 02:47:35AM +0530, Saket Choudhary wrote:
>> Commited a fix here:
>> 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 <firstname.lastname@example.org> wrote:
>> > On Mon, Apr 28, 2014 at 9:07 PM, Saket Choudhary <email@example.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