Hi Andreas, Thanks for the email. We would love to get Gubbins into Debian Med which would simplify the installation process somewhat.
To answer some of your queries: Yes I'd be interested in joining the Debian Med team,
We have written permission from Tal to use his code, but have not discussed licensing. Do you have any advise on convincing people to release their code under a free licence?
The latest version of fastml is version 3, however its an order of magnitude slower than version 2. So we use version 2. To complicate matters, we have patched the codebase to expose some additional functionality and fix some bugs. All changes from the original code are tracked in github. Its an essential part of the software so we cannot do without it.
We noticed the change in DendroPy the other day and its on our todo list to update our code to support the new method names.
We can update to Python 3.
Regards, Andrew
Hi Gubbins developers,
I'm writing you on behalf of the Debian Med team that has the objective
to package all software that might be relevant in the fields of medicine
and biology. We have received a request to package Gubbins from a user
and thus we have put it on our todo list[1].
I noticed that Andrew Page has dropped some packaging stuff into the
download tarball. Since I intended to keep the history I kept his
changelog entries and added Andrew to the Uploader field in
debian/control. Feel free to checkout the current packaging from
the official Debian development platform[2]. Andrew, you are more
than welcome to join the Debian Med team and take part in the effort
to make Gubbins an official Debian package.
When trying to create the package I stumbled upon some issues I would
like to discuss. At first I'm a bit concerned about the usage of
fastml2. The problem is that this is not Free Software and according
to the license that says:
This repository provides some additional functionality to fastml to allow it to
work with Gubbins. The original code is available from
http://fastml.tau.ac.il/source.html and should be your first port of call. To
modify the original code, or use parts of it for other purposes, permission
should be requested. Please contact Tal Pupko: talp@post.tau.ac.il
the fastml author needs to be contacted. I wonder whether you got a
permission from the author for using it in Gubbins. It would be great
to hear that Gubbins is not fully depending from fastml2 and this code
might provide only some extra functionality that in worst case could be
skipped. In any case it might make sense to discuss the license of
fastml with its author - may be he might consider a really free license
which would relax things. One of the results would be that we could
provide an official Debian package of fastml / fastml2.
I found another issue with DendroPy which is listed in the file
INSTALL.md as
* DendroPy ( >=3.11.1 )
While I noticed that this is not part of the (Build-)Depends in the
Debian packaging I started to package it in python-dendropy[3] and
sended a mail about test failures to its authors[4]. When ignoring the
test failures of the python-dendropy and building the packages anyway to
enable a build of Gubbins I noticed the following issue in the test
suite of Gubbins that is most probably connected to the fact that
official DendroPy has released a new major version (4.0.2). I've just
attached the output of the test suite to this mail and may be you could
comment on this.
BTW, the current Debian policy is to refuse software that is Python 2
only. So it would be great if you could either fully migrate to Python
3 or provide support for both Python versions. I have made good
experiences with the script 2to3 to do the Python2 -> Python3
conversion. Please let us know if you are interested in doing this but
might need any help.
Kind regards for providing Gubbins as Free Software
Andreas.
[1] http://blends.debian.org/med/tasks/bio#gubbins
[2] https://anonscm.debian.org/cgit/debian-med/gubbins.git
[3] http://blends.debian.org/med/tasks/bio-dev#python-dendropy
[4] https://lists.debian.org/debian-med/2015/06/msg00063.html
--
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<gubbins-test.log>
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The Wellcome Trust Sanger Institute is operated by Genome Research
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