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

[Michael Crusoe]

On Fri, Aug 10, 2012 at 2:54 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> 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).

Fantastic

>> 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.

Great. I can't find a way to download a recipe from someone else's
PPA. And pointers?


>> > > 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
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