Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)
On Wed, 19 Mar 2014, Carlos Borroto wrote:
> > I lost some of my initial excitement about contributing to Debian Med.
> > If I cannot use the results of my effort in the system where I
> > actually do my job
> quick side question: which are running.... ?
> Are you asking about systems using a lot of software already packaged by
> Debian but not using APT(at least not with the oficial repository) to
> install such software?
;-) something like that. I just was aiming at more specific pointer,
e.g. distribution/release, since that would also add to the picture.
E.g. using some stable but old(er) release of Debian or Ubuntu might
indeed demand users to get fresh versions installed manually (or from
non-official repositories, such as the ones you use or neuro.debian.net)
> Beside the two big ones I already mentioned, Galaxy and CloudBioLinux, I
> don't know any other good example of a popular system for computational
> biology not using official packages. I also don't know of an example of a
> system that does. BioLinux, from where CloudBioLinux comes, is a close,
> but my experience is that the collaboration is not as close as you would
> expected.
> I have also used several institutional HPC clusters, some that are mainly
> used for computational biology and run on Debian or Ubuntu. None relied on
> oficial packages or even APT.
"run on Debian or Ubuntu" but not using packages or APT... oh well -- at
least it keeps some useful admins on a payroll ;) joking aside though,
situation with "institutional" HPC clusters is indeed peculiar, since
they need to address many users from different disciplines, and
even if all the software would be provided by stock distribution, some
users would still demand custom versions and/or builds.
But when we would look at smaller deployments (labs/departments),
starting off with stock distribution/packages could save lots of
human power in the short and long run. Then custom installations could
still be done, using the same 'environment modules' system as they use
across many HPCs.
> Finally, let me repeat myself. I think Debian Med is doing a great job. I
> hope more people could see the benefits of using the official packages. My
> limited involvement allowed me to see how much you can get by following
> good practices for packaging free software. My point was it seems there is
> a need to highlight the importance of these benefits in a meeting like the
> one mentioned in this thread.
+1 ;)
> Also a need for information on how to get
> reproducibility but still use the official packages.
actually that could be the easiest form to achieve kind of
reproducibility: e.g. if someone uses stock release of Debian, as I
have demonstrated, it is very easy to recreate very similar (if
not identical) environment in 1 (or few) commands (such as debootstrap).
--
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate, Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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