Hi Enis!

Thanks for clarifying. One thing I can not find out is or Brad's scripts are installing the packages on system level or in a specific directory (like $GALAXY_APPS/package/version/). Suppose they are installed on the system level, how do you keep track of different versions?

Thanks,

Mattias

On Mon, 2011-09-05 at 14:49 +0200, Enis Afgan wrote:

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, 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