(please CC me, I'm not subscribed)
I've started talking to Alin to see whether more scientific software would be
nice to have in openSUSE. In particular, one of the cool new features of the
day (TM) in the life science sector is the so-called "Next generation
sequencing", and a lot of software has been developed to deal with such
Most of these are command-line tools and some have... "exotic" build systems,
so having them packaged would be definitely a plus for any scientist that's
doing work in the field.
While starting to work on such things myself, I noticed that a number of
packages exist in openSUSE Build Service, but not in the science repository.
Thus, after talking with Alin, it is our idea to have the author of the
repository SR those to the science repo, and package the rest.
Advantages? More openSUSE usage in the scientific field ;)
Of course, more helping hands are always welcome.
The list so far of things that we would strive to get included is:
bowtie (packaged in home:dipe)
bowtie2 (not packaged, needs to co-exist with bowtie, http://bowtie-
bwa (packaged in home:dipe)
tophat (packaged in home:dipe)
cufflinks (not packaged, http://cufflinks.cbcb.umd.edu/
samtools (packaged in home:dipe)
pysam (python bindings to samtools, not packaged -
HTseq (not packaged, http://www-huber.embl.de/users/anders/HTSeq/
FastX toolkit (not packaged, http://hannonlab.cshl.edu/fastx_toolkit/
BEDTools (not packaged, http://code.google.com/p/bedtools/
pybedtools (depends on bedtools, not packaged,