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

[Andreas Tille]

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: © 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

-- 
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