Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)
On Wednesday, March 19, 2014, Yaroslav Halchenko <debian@onerussian.com> wrote:
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?
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.
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. Also a need for information on how to get reproducibility but still use the official packages.
Best regards,
Carlos
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