Hi Carlos,

Yes, I'm an active member of Deb Med but unfortunately not finding time
to read the mailing list properly nor to actually run Debian (or even
the Ubuntu development release).

We've actually factored time into the packaging project to contribute
all relevant packaging into the Debian-Med repositories.  This has to be
done with a bit of care as there are now real differences between
standards for Debian Sid and Ubuntu LTS for which we are packaging.  My
plan is to complete a bunch of packages and then review and commit what
we have in a batch later this month.

I do have a package for TopHat in my own PPA that I added late last

I made a couple of tweaks to get the thing to link properly, but again I
need to check that these aren't Ubuntu specific before I push any
patches back to Alex, who seems to be actively committing changes to Git
right now.



On Wed, 2012-01-04 at 20:22 +0000, Carlos Borroto wrote:
> On Tue, Jan 3, 2012 at 11:36 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> > On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
> >
> >> Dear Galaxy Developers,
> >>
> >> We work in Professor Dawn Field's group (Molecular Evolution and
> Bioinformatics Research Group) at the NERC Environmental
> Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology
> (CEH) Research Institute based in Oxford.
> >>
> >> We develop and distribute Bio-Linux
> (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu
> distribution that comes with 500+ bioinformatics packages. Within our
> research group we also provide bioinformatics analysis for NERC-funded
> researchers, and recently started looking into Galaxy as well. It
> didn't take us long to discover its power and we would like to enable
> Bio-Linux users to install, run and maintain the Galaxy server with
> minimal effort, also with the aim to spread the word on Galaxy in
> Europe!
> >>
> >> Recently we took on a project with Dr. Casey Bergman from
> University of Manchester as the Principal Investigator, to package all
> the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many
> pre-requisities are already included with Bio-Linux, we are already
> some way down this path. New packages that we create will appear in a
> Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy).
> >>
> >> We will be happy to hear any comments regarding these efforts and
> we hope that this will be a useful resource for all Galaxy users. Once
> the initial packaging is done, we hope to collaborate with Galaxy team
> in maintaining and improving this resource.
> >>
> >> Best wishes,
> >> Tim, Soon and Mesude
> >
> > Hi Mesude,
> >
> > This is fantastic, thanks for letting us know, and please do post up
> if there is anything we can help with.  Also, if you're not aware,
> Galaxy's cloud offering is built on CloudBioLinux, which itself is
> built on Bio-Linux.
> >
> > --nate
> >
> This is very good news, I'm personally a big fan of avoiding as much
> as possible installing from source on production systems, as things
> can get easily out of hand when trying to keep everything updated.
> Mesude, I recently joined Debian Med
> (http://www.debian.org/devel/debian-med/ and
> https://launchpad.net/~debian-med) which the exact same goal of
> getting as much tools as possible packaged for Debian/Ubuntu. I see
> Tim Booth is an active member in Debian Med and I was wondering if
> your group is planning to keep the development of these packages in
> the git/svn repositories of Debian Med. I wouldn't want to duplicate
> your efforts.
> I like very much the use of PPAs while waiting for packages to be
> officially included in Debian and trickle down to Ubuntu, process that
> could be somehow slow at times. Just today I was able to upload
> Tophat's package being developed at Debian Med to the PPA, I'm pretty
> sure it needs more work, but you might be interested in taking a look.
> Kind regards,
> Carlos

Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

+44 1491 69 2705

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