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

[Andreas Tille]

Hi Michael,

I'd like to give some update from my side to Steffens mail below.  The
Debian Med team tries to do open conversation (in contrast to private
discussion with long CC list).  I have some record of prefering this
policy over netiquette after having checked that there is no private
content in the mails - I hope nobody of the posters below will mind if I
entertain this habit again here.

As a general hint I would (strongly) advise to read the Debian Med policy
document

    http://debian-med.alioth.debian.org/docs/policy.html

which patiently explains what mailing lists to subscribe and how to
become a member of the alioth team which is finally what you want to
join if you want to touch packages like tophat and qiime (as Steffen
wrote as well).  Working for Ubuntu is fine but we established a
workflow which fixes problems at the root which lastly is Debian.  If
you need some more detailed introduction feel free to ping me about
Mentoring of Month

    https://wiki.debian.org/DebianMed/MoM

(some time of August is left and it seems you just have some packaging
skills so this might fit.)

Specifically regarding Qiime:  I just fixed two bugs reported by Charles
in Debian unstable recently (Mon, 06 Aug 2012).  You are well advised to
consider these changes because I'm not sure how fast these changes might
proceede to Ubuntu and you probably do not want to spend your time on
outdated packaging code (did I said that we are fixing problems at the
root?)

If you have further questions feel free to ask.

Kind regards and thanks for your interest in Debian Med

      Andreas.

On Fri, Aug 10, 2012 at 08:57:59AM +0200, Steffen Möller wrote:
> Hi Michael,
> 
> thank you for the introduction to your interest. I am CCing a few folks
> from Debian Med. Tim has some fame for his preparation of BioLinux.  And
> he is our man for qiime, seconded by Charles, if I got this right.
> Please sync with them. The new packages of yours would be great to see
> co-maintained on the Debian Med svn/git repository. For that you'd need
> an account on alioth.debian.org, which we then add to the Debian Med
> alioth project.
> 
> Many greetings
> 
> Steffen
> 
> On 08/10/2012 12:04 AM, Michael Crusoe wrote:
> > Hello Steffan,
> >
> > I was going to submit a patch for building v2.0.4 of tophat on Ubuntu
> > but it looks like that was already fixed in the packaging repository
> > (though not pushed to Debian unstable yet).
> >
> > I did have to rebuild arb for Ubuntu. I'd be happy to write a recipe
> > to build arb for the DebianMed PPA.
> >
> > 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 would like to help with the quality of the Qiime package as we
> > weren't able to make it match the capabilities of installing it via
> > the app-deploy script
> >
> > On Thu, Aug 9, 2012 at 2:34 PM, Steffen Möller <steffen_moeller at gmx.de> wrote:
> >> Hi Michael,
> >>
> >> I just saw your request to be added to the DebianMed PPA. What packages are you after?
> >>
> >> Cheers,
> >>
> >> Steffen
> 
> 

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