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Last modified 23 months ago Last modified on 04/06/17 12:38:05

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:

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

http://docs.uabgrid.uab.edu/wiki/Galaxy#Next_Gen_Sequencing_Software_.28order_of_install_on_.22cheaha.22.29

UAB Galaxy Mailing Lists

Following is a list of UAB's galaxy mailing lists, all of them are publicly readable (public archives):