Debian packages for the SMRTAnalysis suite (and Python3 compatibility)
Hello,
I'm contacting you on behalf of the Debian Med team, a group within the
Debian project that packages software for biology and medicine. You can
find a list of our work on biology software projects at
http://blends.debian.org/med/tasks/bio
I've taken up the task of bringing in the SMRTAnalysis suite and its
dependencies as a set of official Debian packages. pbcore has already
been included into Debian [1]. pbh5tools is next in that dependency
chain [2]. I've also been working on bringing in Celera Assembler; its
own dependency kmer has been packaged and is awaiting processing by the
Debian ftpmasters [3].
Besides just notifying you of the effort, I'd like to note that it will
be difficult to include into Debian new Python packages that do not
support Python 3 [4-5]. For pbcore, I have made the transition myself[6]
with the intent to forward the patches. Since this will be an issue with
the other Python packages comprising SMRTAnalysis, I would like to see
if we can cooperate to support Python3. I can help with the first step
of the transition, but would you be willing to maintain compatibility
with both Python2 and Python3 versions?
Thank you very much for providing SMRTAnalysis as unrestricted software.
I am personally a regular user of this software.
Many thanks and regards
Afif
1. https://packages.qa.debian.org/p/python-pbcore.html
2. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787982
3. https://ftp-master.debian.org/new/kmer-tools_0~20150520%2B2004-1.html
4. https://wiki.debian.org/Python/StretchRoadmap
5. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=783833#10
6.
http://anonscm.debian.org/cgit/debian-med/python-pbcore.git/tree/debian/patches/modernize-python.patch
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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