Question: Import Local Files
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gravatar for Ryan Golhar
7.6 years ago by
Ryan Golhar80
Ryan Golhar80 wrote:
Hi - I recently discovered Galaxy and am just getting started with it... I installed a local instance to test with NGS data. 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. 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? 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
galaxy • 757 views
ADD COMMENTlink written 7.6 years ago by Ryan Golhar80
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