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

[Ivan Efremov]

Hi Andreas,

> 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.  

I see your point, but most of 3rd-party plugins including ball, hmmer,
phylip, psipred etc. are integrated into UGENE at the source level.
Typically that means that we modified the original code, provided adapters
and so on. For instance, you can take a look at HMMER3 code in the UGENE
tarball - it differs significantly form the original (e.g. we had to replace
all abort()'s and exit()'s). So for tools contained in src/plugins_3rdparty
there is almost no way to reuse original binaries.

The good news is that we have a bunch of algorithms integrated as truly
external tools, i.e. UGENE depends on the original binaries (see
http://ugene.unipro.ru/external.html). In this case we can modify
ubuntu/debian installer to "recommend" these packages and at the source code
level check if needed binaries are installed to system-wide directories.

So, may I ask you to file a bug at http://ugene.unipro.ru/tracker to make
sure our engineers will handle the issue with external tools?


Thanks,
Ivan

> -----Original Message-----
> From: Andreas Tille [mailto:andreas at fam-tille.de]
> Sent: Friday, November 23, 2012 4:39 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
> 
> 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
> 
> 
> --
> http://fam-tille.de