Re: Homepage of LibMems?
On Sat, 16 Feb 2008, Aaron Darling wrote:
Hi Andreas, it's wonderful to hear that you are packaging libMems/Mauve etc
for debian-med!
... so I take the freedom to reply to your mail on the public mailinglist
to enable other interested persons to follow this issues (even if netiquette
forbids publishing private mails - but I think there was nothing private in
it).
As you surmised, there is no explicit homepage for libMems, although
subversion source code repositories for libMems and all the other support
libraries associated with Mauve can be found at:
http://mauve.svn.sourceforge.net/svnroot/mauve/
We also have API docs for these packages here:
http://gel.ahabs.wisc.edu/apidocs/
Yes - I found both links from the docs.
libClustalW and libMUSCLE are versions of clustal-W and Muscle that have been
engineered into software libraries. As such, they are derivative works of
the original softwares and should inherit the licensing from the original
codes. It seems I have mistakenly included a GPL notice in libClustalW.
I might like to point out that perhaps a solution for the license issue
is at horizon. Please read
http://lists.debian.org/debian-med/2008/02/msg00149.html
Regarding the code it might be possible thet clustalw is not needed at all
http://lists.debian.org/debian-med/2008/02/msg00152.html
I would recommend to follow the issues on the Debian-Med mailing list
archive. Sometimes it happens that posters forget to CC possibly not
subscribed interested persons.
I
no longer recall what the original license states, but I will take care to
restore it in the package (thanks for pointing this out!) libMUSCLE is based
on the MUSCLE aligner v3.6, and contains several bugfixes and features not
available in the main muscle distribution. Muscle was released public
domain, so libMUSCLE inherits a public domain license.
Well, the license in principle permits this strategy. On the other hand
one goal of the Debian-Med project is to prevent people from forking by
providing the best and most feature rich software to fit the needed applications.
In this aspect we would have liked it more to contact the MUSCLE authors
by sending them a patch. I hope that the author of the muscle package
in Debian will be able to sort this out. We would be happy if this would
support your work in Mauve.
All of these libraries are basically just support libraries for mauveAligner,
progressiveMauve, and the related C++ programs. Initially I had hoped that
other developers might pick them up and use them in separate projects,
however that seems to not have been the case.
I'm in very favour of this approach because factorizing software in
pieces of separate libraires is a very good strategy to involve more
developers. I would like to support your intention to maintain these
libraries and that's why we try to start these libraries in Debian.
Actually I startet with libGenome. (I had some technical trouble with
this but that's an issue for a different thread[1].)
For ease of building and
maintenance I am now considering pushing libGenome and libMems and
mauveAligner together into a single source tree, and eliminating the
dependency on libClustalW since it is obsolete anyways. I could of course be
persuaded otherwise :-)
Well, I think if libClustalw is not really needed I would prefer to
leave it out because of the license issues and because there seems
to be development in parallel. It would reduce the number of forks
by one and thus would be reasonable.
I'd vote against merging the others. If you ask me the very simple
web page for libGenome perfectly does the job. It just has to be updated
to not point to old versions. If you dare about maintaining it to
keep version numbers up to date, just do not mention the version number
and point to the download directory of the web server, the SVN repository
and the API docs. This would be perfectly sufficient to keep people
informed while freeing you from the work to update the page from time
to time. Alternatively using the SourceForge repository could
perhaps save some time - but that's your decision.
In the meantime, I would suggest if possible that you simply refer to the
Mauve homepage as the homepage for libMems, libGenome, and the other support
libraries. Perhaps it is poor form on my part to have created freestanding
libraries without associated webpages, but it turns out that I just haven't
had enough time to do it. My role has shifted in recent years from being
primarily a software dev to doing scientific research...
No problem - that's kind of known to many of us.
In any case, let me know how the build goes and if you run into any snags. I
have made some changes in the latest subversion code that requires
as-yet-undocumented changes to the build process, so perhaps better to stick
with the release versions for now. The 2.0.0 release seems to have worked
quite well for most people, there are some lingering issues with the 2.1.1
release that I still need to fix.
Many thanks for your input and the intent to work together with Debian-Med.
Cheers,
-Aaron
Kind regards
Andreas.
[1] http://lists.debian.org/debian-med/2008/02/msg00160.html
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