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.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
> 
> 


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

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