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 <[email protected]> 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 <[email protected]> wrote: >> > On Mon, Apr 28, 2014 at 9:07 PM, Saket Choudhary <[email protected]> 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/CAEDHeitnd9hDotJkbuEJBfM9Qg=quhv3vspkfmgv3p2pqp6...@mail.gmail.com
