Hi Mattias,
We use a combination of mi-deployment and Brad's cloudbiolinux script (
https://github.com/chapmanb/cloudbiolinux) to install tools (including the
biolinux ones). It requires some manual effort but has worked for us. The
approach you describe sounds pretty good for packaged tools, I would just
suggest to maybe create a script to automate the process as you go about
installing all of the tools. If you decide to create the script, please
conside sharing it.

Good luck,

On Mon, Sep 5, 2011 at 2:22 PM, Mattias de Hollander <
m.dehollan...@nioo.knaw.nl> wrote:

> Hello Galaxy-developers and community,
> I would like to ask your advice on installing software. I used the
> cloudman scripts to install galaxy on a multi-core server. I use the
> fabric scripts from cloudman/mi-diployment to install some software but
> I am also looking at repositories like biolinux and the NBIC RPM
> repository.
> There has been a thread about that over here:
> http://gmod.827538.n3.nabble.com/RPM-repository-for-NGS-tools-in-Galaxy-tp2617820p2617820.html
> As James says in that thread I also prefer to install software in
> isolated directories to keep track of different version. Did someone use
> the biolinux repository to install software in a galaxy accepted path:
> $GALAXY_APPS/package/version/? How does the Galaxy Cloud team does that?
> (Enis?)
> I was thinking to use 'sudo apt-get --download-only' to first get the
> debs and then install them using 'dpkg --instdir' and then specifying
> the directory. Or is there a smarter way to do this?
> Any thoughts on this issue are appreciated.
> Thanks.
> --
> Bioinformatician
> Netherlands Institute of Ecology (NIOO-KNAW)
> Wageningen, the Netherlands
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