[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: I want to colaborate with debian-med


I happened to have been working on 3.17 myself over the weekend, too.

The upstream makefiles are indeed a bit difficult. This is particularly
so since they
were not aware of make -C nor of () around a chand directory and
therefore upstream used full paths for everything which also made it
into the scripts via sed. I have addressed that, it seems to kind of
work, though I have not tested it yet.

Adrian, if you went along the same lines, then fine, otherwise I would
very much like to ask you to accept some patches of mine, which I am
confident upstream to accept them as well. Adrian, once you have
finished the packaging, please send the diff to Stefan Kurtz in Hamburg
and Steven Salzberg at TIGR, both I have contacted earlier and they are
very much aware of Debian, sending them greetings from us and the
.diff.gz.  Hamburg I know to be infected with SuSE, though. Please have
a look at my attached diff and incorporate the patches to your liking. I
also happily offer my comaintenance of your package.

Referring to the problem of Andreas Annotate in the tigr folder is
indeed strange, ldd denies it to be dynamically linked. It is linked
just like the others, too, though:

  moeller@latitude:/mnt/hda1/home/moeller/src/mummer/mummer-3.17$ ldd
        not a dynamic executable
  moeller@latitude:/mnt/hda1/home/moeller/src/mummer/mummer-3.17$ file
  bin/annotate: ELF 32-bit LSB executable, Intel 80386, version 1
(SYSV), for GNU/Linux 2.2.0, dynamically linked (uses shared libs), not

Our group was invited to write a review article on comparative
bioinformatics and autoimmune disease, in spite there not being too much
to review yet. I thought of mentioning Debian a few times, partially
because of MUMmer and other nice tools ready to use in there, therefore
my renewed interest in this package. :-)

I got the debs now, though only by commenting out the dh_shlibdebs script.



libsbml - I got a _very_ nice package for an earlier version of SMBL
that also found the appreciation of the upstream developers, the later
ones do not compile smoothly, reported that, need to check again.

limma - I got a package for that and for most other R-bioconductor
packages. There is a combined effort addressing CRAN and Bioconductor as
a whole at http://alioth.debian.org/projects/pkg-bioc

you found my inofficial packages of mine for cluster3

you have not found my packages for primer3 , coiled-coil, t-coffee,
tigr-glimmerhmm (which was uploaded but rejected sind some binary files
were found to be installed to /usr/share, should be fixable). Andreas,
you uploaded t-coffee, haven't you?

wise2 is tricky since its compilation depends on an earlier version of
itself, this holds at least for the later versions in CVS, not for 2.2,
for what I overserved.

Attachment: mummer_3.17-1.diff.gz
Description: GNU Zip compressed data

Reply to: