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.

Enis

On Mon, Sep 5, 2011 at 2:22 PM, Mattias de Hollander <m.dehollander@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