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

[Michael Crusoe]

On Fri, Aug 10, 2012 at 12:45 AM, Andreas Tille <andreas at an3as.eu> wrote:
> 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.

Sure, I am a big fan of open conversations.

> As a general hint I would (strongly) advise to read the Debian Med policy
> document
>
>     http://debian-med.alioth.debian.org/docs/policy.html

Done

> 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

As a decade plus user of Debian and Debian derivatives (and often a
sysadmin of the same) I'm very happy to fix problems at the root.

> (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 outdated packaging code (did I said that we are fixing problems at the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?)

Thank you for the heads up. Does Qiime now pass its own self-tests out
of the box on Debian unstable?

> If you have further questions feel free to ask.

Certainly

> Kind regards and thanks for your interest in Debian Med

You are very welcome; 'tis my pleasure to contribute.

>       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
>>
>>
>
> --
> http://fam-tille.de