Ryan Golhar wrote:

Hi - I recently discovered Galaxy and am just getting started with it... I installed a local instance to test with NGS data.

Hi Ryan, I moved this over to the galaxy-dev list since it involves a local install.

We have a lot of NGS datasets (both Solid and illumina) on a SAN available via NFS. Each user that has data has an account on the system in a directory tree such as:

/ngsdata/user1 /ngsdata/user2 /ngsdata/project1 /ngsdata/project2

where user1 and user2 are distinct users with their own dataset, and project1, project2 contain datasets shared by multiple users.

I want to import this data in Galaxy and I came across this thread in the mailing list (quoted below).

I set up my Galaxy instance to see this NFS share...btw Galaxy is running as its own user on a virtual machine. The Galaxy user only has read access to this read and nothing else.

If the usernames match your user's email addresses (this could be done with symlinks), users can import their own data, btw. See the user_library_import_dir option.

When I went to import the files by specifying a local system path on the admin user interface, I got errors importing the data. I checked the paster.log file and I saw errors related to galaxy trying to change the permissions of the files to 0644.

Does this mean all the files need to be owned by Galaxy?

No, this would be a bug. There were a number of bugs like this that I fixed a month or so ago. Could you check your Galaxy version? Thanks, --nate

------------------- Old thread:

Hello Andreas,

The best approach to handle this is to have a Galaxy administrator upload the files into a library, creating library datasets. Set the following config setting to point to the NFS accessible directory you use to contain the files:

# Directories of files contained in the following directory can be uploaded to a library from the Admin view library_import_dir = /var/opt/galaxy/import

You can set ACCESS permissions on the library to restrict access to specific users, or leave it public to allow anyone to access the library datasets.

Users can import the library datasets into their own histories for analysis - doing this does not create another disk file, but simply a "pointer" to the library dataset's disk file.

Greg Von Kuster Galaxy Development Team

Andreas Kuntzagk wrote:

...

Hi,

to reduce traffic when importing big dataset into our local galaxy we would like to copy directly from the fileserver (which is accessible from the galaxy server via NFS) into galaxy without moving through the users desktop computer. Is there already such a tool by chance? At a glance I could only find import.py which imports only from a predefined set of files. So if no such tool exist what would be the best starting point? upload.py? For security reasons I would restrict the import to a certain directory. Anything else to keep in mind?

regards, Andreas _______________________________________________ galaxy-user mailing list galaxy-user at bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

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