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

[Tim Booth]

Hi Michael,

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).

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).

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.

> And
> > he is our man for qiime, seconded by Charles, if I got this right.

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.

> > > 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

I didn't need to change much - I think I just had to rename the build
dependencies to match the package names on Ubuntu and to ensure that
Openmotif was available.

> > > Other software I may package at a later date:
> > >
> > > 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
> > > Darkhorse (after I get it to work from scratch) http://darkhorse.ucsd.edu/
> > > mauve http://gel.ahabs.wisc.edu/mauve/

I've not looked at any of these myself.

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.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.