Fedora Core 6&7 support is in trunk to some degree, but I do not believe is
complete. If you want to spend some time fixing it up, then that would be
great. The path we are taking with GSoC is to package for 5.0 and then
convert those packages later, because we have not finalized our process with
the new packaging system in trunk. The documentation in the developer wiki
http://svn.oscar.openclustergroup.org/trac/oscar/wiki/DevelDocs
should be current.
As far as the Bioinformatics package go, Bernard and I have been kicking
this idea around for a while, but neither of us have had the time to make
much progress on it. It was our plan to use the BioBrew rpms, at least as a
starting point, we have even spoken to the maintainers of that project and
they don't mind at all. I would also like to add some additional software,
especially something which adds a user interface of some sort to the system.
I am mentoring several projects for GSoC this summer, so I will be fairly on
task with OSCAR anyway, so I would like to assist with this project.
On 4/12/07, Mattias de Hollander <[EMAIL PROTECTED]> wrote:
Hi all,
I am a BSc (bioinformatics) student and for a project i am going to setup
a 'biological' cluster computer. I've got a few question regarding OSCAR
setup and package creation.
As Linux distribution i'm going to use Fedora. What is the latest version
of Fedora that is (fully) supported? I think that FC5 is still the latest
officially supported distribution, but on this mailing list i read some
threads about installing upon FC6 and FC7. What is the best version to use?
To make the cluster more biological i am planning to install software like
BLAST, ClustalW, contig assembly programs, etc... (with hopefully MPI
support). I saw on the GSoC2007 projects page that a similar project is
listed (OSCAR Bioinformatics Toolkit), so i suppose such system is still
needed, because two years ago another student as worked on this (
http://www.mail-archive.com/[email protected]/msg04121.html
). Am i right? So is there some starting material available and what were
the problems he experienced?
I also looked at creating packages for OSCAR, but the howto i found on the
website seems a bit outdated (2004). I think i read on the mailinglist that
the packaging system for OSCAR 5.0 (and 5.1) has changed. Where can i find
updated instructions for creating packages? Isn't it also possible to
install software on the nodes from a tarball with the C3 tools?
For 'the other cluster toolkit', ROCKS, there exists a roll with
bioinformatic RPMS (BioBrew). Although i prefer OSCAR, are these RPMS not
compatible with OSCAR? (
ftp://ftp.bioinformatics.org/pub/biobrew/srpms/4.1/)
Thanks in advance,
Mattias
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