About EMBOSS
Dear all,
I still wish that we could ship EMBOSS in Etch; here are a few thoughts
about this.
First of all, there is the package of Matt Hope. If properly fixed for
the xlibs transition, it builds fine on Etch. However, it is two major
versions lagging behind the current release. Do you think that it makes
sense to upload it anyway to NEW? The NEW queue is getting long again,
and I do not know if it means that some packages will not make it in
Etch because they will be stuck in the queue before the freeze.
Uploading emboss 2.8 shortly would solve the problem in advance.
In any case, I will try contact Matt Hope today and ask if it is OK if
we take over the packaging. As he seems to be MIA, I do not really
expect an answer, but we never know. One or two weeks later, I will send
a last call on -devel.
However, we may not need to start from Matt Hope's work. There is
another package built by the bio-linux team which is directed by Bela
Tiwari. He wrote two letters in major scientific journals (Nature,
Nature Biotech) to promote bioinformatic free software, and always sent
me friendly replies to my mails. On the other hand, he seems te be very
busy, and the replies take some time to come. Even if we do not want to
start from the bio-linux package, which is likely to be lintian-unclean,
we could benefit from accessing its sources, which are not available for
download. I will ask him to communicate them, but as I really would like
to create a friendly collaboration with his team, I will not _require_
the sources as the GPL would allow me to do so. In any case, the GPL
also allow them to withdraw the binary package from public download, so
there is nothing to win in direct confrontation.
Lastly, I have started some preliminary work on dependancies of EMBOSS.
I have obtained from the REBASE copyright holders the permisson to
distribute REBASE as a debian package, and I have good contacts with the
upstream author of primer3, who is asking his employer (the copyright
holder) to relicence his work under the BSD licence. It was recently
confirmed on -devel that the current licence of primer3 (BSD with
advertisement clause) is officially DFSG-free, mostly for historical
reasons. But this licence is just too easy to infringe by accident by
distributors, so I think that is is wiser to wait the answer from the
copyright holder of primer3 before uploading it to main (there is a
package almost ready made by Steffen Moeller, and I am working on it to
upgrade to the newest version).
I am affraid that this mail is a bit too verbose and long. Buy the take
home message is this quesion:
Who is intersted to paricipate to the packaging of EMBOSS?
I have guests in the two last weeks of september, so it means that I
would mostly work on this in the next two weeks, and the first week of
october. Then I do not know how the freeze process works: it the
packages have to be in testing on the 18th of october, it means that we
must upload emboss before the 8th. Otherwise, we may have some time.
This schedule is very tight. If there are unexpected difficulties, I
think that it is perfectly OK to release Etch without EMBOSS. But I
would be a bit fustrated if I did not at least try.
Have a nice day,
--
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan
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