[Debian-med-packaging] Bug#1009118: python3-biopython: incompatible with muscle >= 5

[Étienne Mollier]

Hi Andreas,

Andreas Tille, on 2022-11-24:
> Am Thu, Nov 24, 2022 at 10:28:43AM +0900 schrieb Charles Plessy:
> > I have read the Muscle5 paper and it is a totally different program than
> > Muscle3.
> > 
> >     https://pubmed.ncbi.nlm.nih.gov/36379955/
> > 
> > Reintroducing muscle3 as a separate package might be useful not only to
> > Biopython, but also to the people who need it in pipelines, etc.
> 
> I've created a new git repository[1] and filed an ITP bug report.  Will
> upload to new soon.

Thanks for the upload, I further adjusted the muscle wrapper so
it would catch the muscle3 binary if it finds it in the path, as
I see your new package provides the executable /usr/bin/muscle3.
If no such executable is available, the default switches to
plain muscle.  In any case it is possible for a user of the
biopython wrapper to enforce a given executable name by setting
the cmd argument of the constructor.  Changes are available in
the muscle3 patch[2] on salsa.  I'm hopeful to upload biopython
1.80 to experimental this evening.

> [1] https://salsa.debian.org/med-team/muscle3 
[2]: https://salsa.debian.org/med-team/python-biopython/-/blob/master/debian/patches/muscle3.patch

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
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Sent from /dev/pts/2, please excuse my verbosity.
On air: Phideaux - Dormouse Escapes
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