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

[Andreas Tille]

Hi,

On Fri, Aug 10, 2012 at 12:59:40PM +0100, Tim Booth wrote:
> There are few outright incompatibilities but there are a few things that
> matter for Ubuntu but not for Debian and vice versa - for example I've
> been tweaking various .desktop files to work nicely in the Unity
> environment (eg for ARB).

I have no idea whether there are incompatibilities between .desktop
files between Debian and Unity.  As far as I know there is just a
freedesktop.org standard and a .desktop files should simply follow this.
In case you consider Debian ignorant about .desktop files this is wrong
- we also would like to have these.

> I've not committed anything back to SVN yet
> as I know Unity isn't a specific issue for Debian but I will, so as to
> keep everything neat.
> On the other hand, I think Debian still wants me to provide entries
> under /etc/menu which I'd not normally bother with for an Ubuntu
> package.

I admit that having something to feed dh_menu with is written in policy
but I can not imagine that this would harm Ubuntu.  In case it would a
lot of Debian packages would have a problem.  So I personally would not
see any need for changing something just because a menu entry is there
(users are free to ignore and as far as I know Unity will do this for
your users anyway).
 
> > 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'm spending more time right now on "problem solving" than on repetitive
> tasks, so auto-building is a nice-to-have but not something that would
> speed up the arrival of BL7.  I am, however, trying to do things in a
> way that can be automated - eg. using build scripts and packages rather
> than making ad-hoc changes.

I admit I know to less about BioLinux - I just could suggest that
talking to NeuroDebian people might be a good idea because I have the
impression that these people have invented some clever things to reduce
workload and to some extend they are doing exactly the same as BioLinux
just for a different user base and with a different set of packages.
 
> > Hint: The new package recommends python-biom-format which is for sure in
> > Debian unstable - you might need to take this over as well. 
> 
> Cheers - Soon also mentioned that to me as he's been using the new Qiime
> (which won't run on BL6 due to needing updated Python) recently.

<nagging>
Hmmmm, Soon.  This name rings a bell.  Wasn't Soon the guy who wanted to
become a MoM student.
</nagging>
 
> > 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. :-()
> 
> I'll have some minor fixes to push but I'm not changing your overall
> setup - it was clearly a heroic effort given how wacky the whole
> codebase is.

You name it.  Pushing anything is fine.

> > 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.
> 
> I'll see what I can do.  One obvious change would be to change the
> default clusterer from uClust to a free alternative.  Qiime does support
> this, but I need to consult the developers on how sensible it is to set
> this by default.

Any enhancement would be great.

Kind regards

      Andreas.

-- 
http://fam-tille.de