[Debian-med-packaging] Bug#693655: ugene: Please update ugene to the latest version 1.11.3

[Andreas Tille]

Hi Ivan,

On Fri, Nov 23, 2012 at 03:19:39PM +0700, Ivan Efremov wrote:
> Thanks for catching this issue.

You are welcome - it is one of the goals of Debian Med project to work
together with upstream as close as possible for a common goal to spread
free software.

> I agree that (2b) works perfectly for us. Technically, it looks trivial to
> split the packages.

That's great.

> We are going to fix our Ubuntu packages. Once this is done it will be easy
> to repackage Debian ones. Basically, this would require moving couple of
> dynamic libraries (phylip and psipred) to a separate .deb.

Phylip is packaged for Debian (and thus also available in Ubuntu).  We do also
have some preparation for psipred in our packaging SVN[1] - so throwing out
packages to non-free should be no real problem (hopefully).

Since you confirmed that it might be technically trivial to split
plugins from Ugene I wonder whether you might support the idea I
expressed in my last mail (see below for the relevant part) to use
Debian packaged versions of those plugins you are providing.  For
instance we do have packaged ball, hmmer2+3, kalign, primer3 and from a
distribution maintenance of view it is a good idea to prevent code
duplication and rather define dependencies to the according packages
(same applies for sure for Ubuntu).  What do you think about this idea.

> I'll post a notification once we are done with Ubuntu packages.
> You can track our progress at
> https://ugene.unipro.ru/tracker/browse/UGENE-1310 

Thanks for the link.  I'll create an according bug report inside Debian
to keep a proper record.

Kind regards

       Andreas.

[1] http://debian-med.debian.net/tasks/bio#psipred 


> -----Original Message-----
> From: Andreas Tille [mailto:andreas at an3as.eu]
> Sent: Thursday, November 22, 2012 4:57 PM
> To: Ivan Efremov
> Cc: 693655 at bugs.debian.org; 'Logan Rosen'
> Subject: Re: Bug#693655: ugene: Please update ugene to the latest version
> 1.11.3
> 
> ...
> Regarding third party components:  We just replaced zlib but there are a
> real lot of plugins readily packaged for Debian.  I'd really love if we
> could modularise ugene a bit more and use the Debian packaged components
> if this is somehow possible.  I'd volunteer to create a list based on our
> pool of biological applications[2] and libraries[3].

> [2] http://debian-med.alioth.debian.org/tasks/bio
> [3] http://debian-med.alioth.debian.org/tasks/bio-dev


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