Hi Ravi,
in a nutshell try to install all tools locally on your computer (same
architecture than your cluster). Copy over all tools and directories.
Now go to every tool-directory and create a symlink from the folder
where the env.sh file is located to a folder called default. For example:
/usr/local/tools/samtools/0.0.19/iuc/package_asdf/34213452345/ (here is
your env.sh file) to /usr/local/tools/samtools/default/
That should work, but your are loosing reproducibility and can't use
different versions of the same tool.
What about running Galaxy in a docker container
(https://github.com/bgruening/docker-recipes/tree/master/galaxy) and
hosting everything there, isolated from your webserver?
Hope that helps a little bit,
Bjoern
Am 14.05.2014 18:43, schrieb Ravi Alla:
Hi All,
Due to the nature of our cluster we are not allowed to have compilers on our
webserver, which is where our galaxy instance runs. Because of this tool
dependencies and tools that need to be compiled fail to install through the
galaxy tool shed webpage. Is there a way for me to install dependencies and
tools manually? For example I am trying to install the GATK2 wrapper. This
depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is
there instructions somewhere as to where to install these tools such that they
are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am
really out of sorts here.
Thank you
Ravi
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