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?



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.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

Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to