Which Useful Debian-Like Repositories Do You Know?

Question

[Geparada]

Hi!

I'm using Ubuntu and recently I have been using a nice bioinformatics source repository:

deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux

Which has tons of useful programs that you can easily download and install from your package manager. I wonder if anybody knows another repository like this.

Thanks!

[Michael Schubert]

..and by debian-like you mean it provides .deb packages?

[Geparada]

@Michael Schubert: yes!

[Ketil]

For Ubuntu, extra software is often contributed in PPAs (personal package archives). See http://www.ubuntugeek.com/where-to-search-ubuntu-personal-package-archives-ppa.html

Answer 1

[Chris Evelo]

Here are the Ubuntu 10.04 and Debian Bioconductor repositories that Tony Travis and Steffen Moeller have built using "cran2deb". Tony did this to support Bioconductor as 'deb' packages under Bio-Linux 6, and eventually to be part of a GenePattern distribution. The Bioconductor 'deb' package repositories are at:

Debian: http://master.dermacloud.uni-luebeck.de/cran2deb/rep/

Ubuntu (X86_64) 10.04 LTS: http://bioinformatics.rri.sari.ac.uk/cran2deb/rep

The "cran2deb" project is at: http://r-forge.r-project.org/projects/cran2deb/

(Thanks Tony, for mailing me these)

BioLinux is also the basis for the NuGO blackbox project that I mentioned in another question. We will clean up the Debian repository we use for that soon and I will add it here.

[Geparada]

nice!... I'll try it. Thanks!

Answer 2

[Casey Bergman]

Max Hauessler when he was in my lab put together .deb and .rpm files for Jim Kent's source tools, but I see from the comments on this post that you have already seen these resources.

[Geparada]

Yes, actually I use these a lot!!! You have a nice and useful lab blog, thanks!

Answer 3

[Casey Bergman]

Debian-Med looks like the motherlode: http://debian-med.alioth.debian.org/tasks/ with lists of packages for general bioinformatics, NGS, phylogenetics, etc., etc.

[Aleksandr Levchuk]

+1 I talked to one of the Debian developers at SCALE this year - he said that packaging CRAN is a major project. Debian 6 (stable) has been released a few months ago but bioinfo pakages are many but most are somewhat outdated.

[Aleksandr Levchuk]

+1 Debian out of all official repositories pack by far the most Bioinformatics tools. One of the Debian developers said to me at SCALE this year that also packaging CRAN R libraries (and I think Bioconductor too) is a large ongoing project. It is a big deal because the most time consuming part in installing R packages are the external software and library dependencies all of which are already packaged in Debian!