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Report from Debian Med Sprint

after Debian Med sprint we had this week-end in Schönberg (22/02 -> 25/02), here is a report about the work I've done during this sprint.
Tasks done were also added to the Sprint wiki page [0]

1. I had committed to work with Andreas on Goby packaging. After a look to the library, it appeared that the source relies on a large number of libraries not available in Debian. Furthermore, at least one of its dependencies is in non-free section. This meant we could not go to the free section as expected (contrib at best).
  To get a clear view on what is missing, I made a list of all used libraries not available in Debian with their upstream location when available [1] (and dependencies of dependencies,...).
  Some deps source could not be (yet) found, and I am afraid that other libraries may cause issues because Goby relies on very old versions.
  We have decided for, at least for moment, that we would include part of those libraries in the package and push it to non-free section.

2. After point 1 analysis, I decided to work on igv (which makes use of goby). A first draft of the package is available. Additional updates and tests need yet to be done to use some Debian available libs originally included in upstream code. Some copyright updates need also to be fixed before upload to non-free.
  A request to Debian-Java has been done to upgrade libbcprov-java (new release is required, #701698).

3. My initial commitments were to work on libgenome-model-tools-music-perl . During the week-end I packaged them in Debian Perl as well as all its dependencies. We decided to keep libgenome-model-tools-music-perl and libgenome-perl in Debian Perl and to simply add Debian Med as additional maintainers.
     - Base dependencies libclass-autoloadcan-perl, libgetopt-complete-perl, libtest-fork-perl have been packaged and are waiting for upload by Debian Perl team.
     - libur-perl, libgenome-perl and libgenome-model-tools-music-perl are ready for upload but waiting for previous dependencies availability for complete testing.

4. Bug squashing
   Fix a bug in beast-mcmc (#698497).

5. Discuss with Christoph Gille about STRAP and proposed my help for Java packaging stuff.

6. A few key signing....

[0] http://wiki.debian.org/DebianMed/Meeting/Kiel2013

[1] https://lists.debian.org/debian-med/2013/02/msg00152.html


gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

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