Useful Scripts and Administration Tricks

This page aims to help ease the burden of administration with some easy to use scripts and documentation on what is available for admins to use.

Uploading a directory into a Data Library

Data libraries can really ease the use of Galaxy for your administrators and end users. They provide a form of shared folders that users can copy datasets from into their history.

This script was developed to be as general as possible, allowing you to pipe the output of a much more complex find command to this script, uploading all of the files into a data library:

$ find /path/to/sequencing-data/ -name '*.fastq' -or -name '*.fa' | python $GALAXY_ROOT/scripts/api/library_upload_dir.py

Find has an extremely expressive command line for selecting specific files that are of interest to you. These will then be recursively uploaded into Galaxy, maintaining the folder hierarchy, a useful feature when moving legacy data into Galaxy. For a complete description of the options of this script, you can run python $GALAXY_ROOT/scripts/api/library_upload_dir.py --help

This tool will not overwrite or re-upload already uploaded datasets. As a result, one can imagine running this on a cron job to keep an “incoming sequencing data” directory synced with a data library.