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BioPython Debian packages uploaded (Was: BWA command line change?)


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:
> 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@googlemail.com> wrote:
> > On Mon, Apr 28, 2014 at 9:07 PM, Saket Choudhary <saketkc@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


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