Galaxy Data Libraries

Galaxy has a concept of 'Data Libraries' which is a data container to organize files in an hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. You can add datasets to a data library by uploading them through a web browser, pasting external URL paths or referencing existing directory in $USER_SCRATCH on Cheaha.

Creating a new data library
Right now Galaxy supports data library creation only for administrative users. You can request a new data library by sending an email to [mailto:galaxy-help@vo.uabgrid.uab.edu UAB Galaxy help list]. Please mention name, description and synopsis (optional) for your new data library. You will have full permissions to manage your data library access.

Accessing a data library
A data library can be accessed by clicking 'Shared Data --> Data Libraries' item in the top menu bar.

Adding datasets to the data library
Data library provides three options to add datasets:
 * Upload files
 * Upload directory of files
 * Import datasets in your current history

Upload files
The first option allows uploading files using a web browser and pasting external URL locations.

Upload directory of files
The second option lists existing directories in $USER_SCRATCH on Cheaha. Click on 'Server directory' drop-down menu to see a list of files in your $USER_SCRATCH. Galaxy application needs read and browse permissions to use this upload option.

Setting permissions on $USER_SCRATCH
Galaxy application needs read and browse permissions on the $USER_SCRATCH and they can be set using Access Control List (ACL): setfacl -m u:galaxy:rx /scratch/user/$USER

Setting permissions on a sub-directory
Galaxy application needs recursive read and browse permissions on a subdirectory that will be copied or linked. This can be done using following Access Control List (ACL) command: setfacl -R -m u:galaxy:rx /scratch/user/$USER/demo-datasets

After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.