[Debian-med-packaging] Debian Med! (Was: Debian Med?)

[Andreas Tille]

Hi Tim,

On Fri, Aug 10, 2012 at 10:54:13AM +0100, Tim Booth wrote:
> I'm currently in the process of rebuilding packages for Bio-Linux 7
> (based on Precise) in order to upgrade all the users of Bio-Linux 6
> (Lucid).

Just let us know if we can help out with this effort.  As far as I could
imagine any change that might be needed should probably work for Debian
as well.
 
> I'd second the advice of Andreas on how to work with Debian-Med and
> especially to try and keep discussion in the open lists if possible
> (though I'm guilty myself of not communicating enough).

You've done your share of communication by organising the sprint this
year. ;-)
 
> In terms of Debian vs. Ubuntu there are various differences between the
> two systems that mean you can't necessarily package for Ubuntu and
> assume everything is right for Debian - but, as Andreas says, you are
> not the first person to come across this issue.

As far as I know about those differences it is because we might be a bit
picky about lintian issues and such things.  My guess is that the
differences which are needed in Precise would be quite small (I'd be
keen to know if I'm wrong here.)

BTW, I could imagine some autobuild process for BioLinux.  I know that
NeuroDebian team does autobuild packages for a set of Debian and Ubuntu
releases.  You might like to talk to them to create BioLinux releases
more effective.  These people are lurking on Debian Med mailing list.
 
> I've just reached "M" on my TODO list of packages so Qiime is right in
> my sights for today.  I have a backported version for Ubuntu Lucid that
> incorporates various fixes but is totally forked from the version in
> Debian Med (as Lucid doens't support the python2 build helper).  Now I'm
> working on Precise I'm planning to grab the latest version from Alioth
> SVN and then see if I need to apply any fixes to it to get the same
> functionality as I had before.  If I see the fixes are also relevant to
> Debian I'll work with Charles to merge them back into Debian.

Hint: The new package recommends python-biom-format which is for sure in
Debian unstable - you might need to take this over as well. 

> > > > I did have to rebuild arb for Ubuntu. I'd be happy to write a recipe
> > > > to build arb for the DebianMed PPA.
> 
> I have a version here:
> 
> https://launchpad.net/~nebc/+archive/bio-linux/+packages

Arb is as well in Debian non-free.  It might make sense to settle with
one single packaging.  I admit I did some things years ago which I would
not do these days.  Please have a look into this and change whatever you
feel worth changing.  (BTW, arb is my most hated Debian Med package -
I never was able to simply build it but always had to deal with certain
issues and patches. :-()
 
> > > >
> > > > jModelTest http://molecularevolution.org/software/phylogenetics/jmodeltest
> > > > dambe (under wine *shudder) http://dambe.bio.uottawa.ca/dambe.asp
> > > > AMOS http://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation

  see svn://svn.debian.org/debian-med/trunk/packages/amos/trunk/

> > > > Darkhorse (after I get it to work from scratch) http://darkhorse.ucsd.edu/
> > > > mauve http://gel.ahabs.wisc.edu/mauve/

  see svn://svn.debian.org/debian-med/trunk/packages/mauve/trunk/

Michael, in general you are good advised to see

   http://debian-med.alioth.debian.org/tasks/bio

before considering packaging something.  Just tell us if you want to see
something added to this list (jModelTest, dambe and Darkhorse are just
missing - please do some research whether there is some packaging stuff
hanging around and we will incorporate it).

> Shall we work together on Qiime just now?  I'll push whatever I make
> today straight to the Debian Med PPA.  If you have your own patches
> already, or just a list of issues, then could you share them?
> One thing to mention is that for Bio-Linux I also install a wrapper
> package:
> 
> http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/bio-linux-qiime_bl1.1.0-9_all.deb
> 
> This adds functionality that for various reasons (mostly non-free
> licensing) hasn't been put into the regular Debian package.  But it is
> worth reviewing - it may be that actually some of the fixes made by my
> wrapper can be pushed into the main package after all.

It would be worth checking.  We should try to reach a zero diff between
Debian Med and BioLinux packaging code if possible.  Perhaps nagging
some upstream about freeing their stuff would be helpful as well.

Kind regards

      Andreas.

-- 
http://fam-tille.de