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

Ivan Efremov iefremov at unipro.ru
Fri Nov 23 08:19:39 UTC 2012


Hi Andreas,

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

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.

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 


Regards,
Ivan




> -----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
> 
> Hi,
> 
> On Wed, Nov 21, 2012 at 09:35:10AM +0100, Andreas Tille wrote:
> > Hi Ivan,
> >
> > thanks for the help - I hope to get the Debian packaging soonish.
> 
> hmmm, I guess that there is some showstopper in getting out the latest
> version soon.  I was updating the debian/copyright file and noticed that
> the tarball does contain two non-free components:
> 
> Files: src/plugins_3rdparty/psipred/src/seq2mtx.cpp
>        src/plugins_3rdparty/psipred/src/sspred_avpred.cpp
>        src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp
> Copyright: C 2000 D.T. Jones <dtj at cs.ucl.ac.uk>
> License:
> ...
>  1. The User will receive the Software and any related documentation in
>     confidence and will not use the same except for the purpose of their
> own
>     research. The Software will be used only by such of the User's
> officers or
>     employees to whom it must reasonably be communicated to enable them to
>     undertake their research and who agree to be bound by the same
> confidence.
>     The User shall procure and enforce such agreement from his or her
> staff for
>     the benefit of the Copyright holder.
> ...
>  3. All forms of the Software will be kept in a reasonably secure place to
>     prevent unauthorised access.
> ...
>  6. The Software may not be sold as a standalone package, or incorporated
> into
>     a commercial software package without the written permission of the
> Copyright
>     holder. The Software may be used freely for individual academic or
> commercial
>     research. The Software may also be made freely available for training
> or
>     teaching purposes.
>  .
>  7. The results produced by the Software may not be incorporated into any
>     data banks or databases which are subject to the payment of access or
>     license fees without the written permission of the Copyright holder.
>  .
>  8. The Software may be made available to users over a local network or
>     wide area network (including the Internet), but only if access is
> granted
>     free of charge to all authorised users. Incorporation of the Software
> into
>     a commercial Web site or other fee paying service is not allowed
> without
>     the written permission of the Copyright holder. If PSIPRED results are
>     returned to the user via such a network service, then a suitable
>     acknowledgement of the PSIPRED method must be returned somewhere in
> the
>     output text.
> ...
> 
> 
> That's all pretty non-free.
> 
> Moreover the source does contain a copy of phylip which we all know is
> non-free (and you might even like to try signing a petition to convince
> the
> authors freeing their code[1].)
> 
> 
> So what can we do?
> 
>    1. Move whole Ugene package to non-free (simple but gutless)
>    2. Splitting those non-free parts from tarball and use Debian packaged
>       code (from non-free - we do have at least phylip there and could try
>       to package psipred as well if urgently needed).
>       Then it depends from the fact whether
>        a) component is urgently needed by ugene and we need to add a
>           Depends/Recommends -> ugene needs to go to contrib
>        b) ugene runs fine without thes components and these are just an
>           enhancement -> ugene remains in main and just Suggests those
>           non-free components
> 
> I'd consider 2b) the ideal situation but I can neither decide about the
> relation between ugene and those modules nor do I know whether the split
> is technically easily feasible.
> 
> 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].
> 
> Kind regards
> 
>       Andreas.
> 
> [1]
> https://wiki.debian.org/DebianMed/Meeting/Southport2012/ePetition_Phylip
> [2] http://debian-med.alioth.debian.org/tasks/bio
> [3] http://debian-med.alioth.debian.org/tasks/bio-dev
> 
> --
> http://fam-tille.de



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