Which Useful Debian-Like Repositories Do You Know?
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10.5 years ago
Geparada ★ 1.4k

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!

linux bioconductor • 5.0k views
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..and by debian-like you mean it provides .deb packages?

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@Michael Schubert: yes!

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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

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7
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10.5 years ago

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.

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

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4
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10.5 years ago

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.

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

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10.4 years ago

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

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+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.

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+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!

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