Hi Donny,
Galaxy expects data to be "copied in" to its data store (by default,
galaxy-dist/database/files/), and it's not designed to access data in
the way you're suggesting. However, there are some workarounds.
First, if the data is added to a Data Library (an admin feature,
although once a library is created, non-admin users can be given write
access to specific libraries), data can be "uploaded" to libraries
without copying it in to Galaxy. This is documented here:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
The Galaxy user must have read access to the data in question to be imported.
Datasets in Galaxy can also have their path set explicitly, a feature
which some Galaxy admins have used to create a Galaxy tool that allows
users to browse their local filesystem space and "import" datasets
without copying them.
Hope this helps,
--nate
On Thu, Dec 19, 2013 at 3:23 PM, Shrum, Donald C <dcsh...@admin.fsu.edu> wrote:
> Hi,
>
> I'm at the Florida State University HPC and setting up an a Galaxy server
> that will be used to submit jobs to our HPC cluster. I'm using apache as a
> proxy for the Galaxy server and I'm in the process of setting up ldap
> authentication.
>
> I had planned to mount our HPC file system (with user home directories) on
> the Galaxy server so that users would have access to their data but I'm
> wondering if I have the wrong idea about how Galaxy works and if there is a
> way to map users to their home directories in Galaxy easily.
>
> Thanks for any pointers.
>
> Donny Shrum
>
>
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