Table of Contents
Galaxy @ UAB
The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on Galaxy, backed by the Cheaha compute cluster, and powered by UABgrid. Documentation on the UAB installation can be found on the UAB Galaxy wiki.
Users
Our user oriented documentation and tutorials are available on Research Computing user wiki If you have any questions or need help in running your analysis, then you can contact UAB galaxy experts using UAB galaxy users mailing list. List user documentation related pages here (user doc should go on the docs wiki as well):
Source code
Our UAB galaxy instance includes some customizations to tool-wrapper settings and other misc. scripts. Our source code is maintained in a Git repository hosted on git.uabgrid.uab.edu . Anyone having a user account on the git.uabgrid.uab.edu system should be able to clone it using following git-ssh command:
$ git clone ssh://$USER@git.uabgrid.uab.edu/home/git/repositories/galaxy.git
The UAB galaxy source code is obtained from the upstream development repositories - galaxy-dist and galaxy central. The source code is routinely updated from galaxy-dist repository and occasionally important bug-fixes and features are fetched from the galaxy central repository.
Developers
List developer documentation here:
- Getting started as a new admin
- Setting up a personal instance and contributing changes
- HTTPS Certificate Renewal and Installation
- Making config file changes
- Merging upstream releases with our repo
- Pushing major releases
- Git based deployment
- Database configuration
- Misc. enhancement scripts
- galaxy-init-script - scripts/galaxy-init-script
- galaxy-annce subscription - scripts/get_uab_users.py - Subscribe new users to galaxy-annce mailing list - runs as a cronjob on galaxy VM as galaxy system user
- importfs setup - scripts/ensure_importfs.rb - Create importfs dirs for new users - runs as a cronjob on Cheaha head node as galaxy system user
- failed job notifications - scripts/report_failed_jobs.py - report false positives - runs as a cronjob on galaxy VM as galaxy system user
- Running galaxy tools from command line - NOT API
- Overview of file uploads
- List of Applications Requested for Galaxy Integration
- Sending patches to upstream
- Creating demo tools
Deployment and directory structure
Moved this section to a separate wiki page - DirectoryStructure
Shared Data
Not yet done, the idea is to share public data sets between (at least) SSG and CCTS.
Galaxy Installation
Moved this section to a separate wiki page - GalaxyToolsInstallation
Prior work on galaxy tools installation
UAB Galaxy Mailing Lists
Following is a list of UAB's galaxy mailing lists, all of them are publicly readable (public archives):
- UAB galaxy developers mailing list: Mailing list for UAB galaxy developers discussion
- UAB galaxy users mailing list: Mailing list for users - support, feature request and general user experience related discussions
- UAB galaxy announcements mailing list: UAB galaxy announcements like service status and system updates are sent to this mailing list
- UAB galaxy trac notifications mailing list: Trac wiki's ticket update notifications are sent to this mailing list
- UAB galaxy errors mailing list: Errors reported using galaxy web interface are sent to this mailing list
