From Cheaha
Jump to navigation Jump to search

Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team


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.


The UAB Galaxy instance can be accessed at using BlazerID credentials. The https/ssl access will be available soon. The UAB Galaxy instance is using revision 50e249442c5a from the upstream galaxy repository.

[Temporary Protocol for moving large sequence files (>2GB) to UAB's galaxy instance (or very large numbers of files).


Behind the scenes the Galaxy server at UAB is powered by Cheaha cluster.

Available Tools

Following is a list of tools available through Galaxy platform right now. More description will be added soon.

Software Version Information
bwa 0.5.9 Further information
bowtie 0.12.7 Further Information
lastz 1.02.00 Further information
samtools 0.1.12a Further information
Legacy blast (megablast) 2.2.25 Further information
srma 0.1.15 Further information
velvet 1.1.03 Further information
Top Hat 1.2.0 Further information
Cuff Links 1.0.1 Further information
Lift Over 26-Apr-2011 18:26 2.6M Further information
R R-2.13.0 Further information
RPy 1.0.3 Further information
ps2pdf ?? Further information
MACS 1.4.0rc2 Further information
taxonomy2tree r3 Further information
sputnik NA Further information
beam2 Unknown Further information
addscores NA Further information
clustalw 2.1 Further information
gmaj NA Further information
gpass NA Further information
HYPHY 2.0020110330 beta Further information
laj NA Further information
pass2 NA Further information
twoBitToFa NA Further information
Perl revision 5 version 8 subversion 8 Further information
perM 3.3 Further information
GNUPlot 4.4.3 Further information
Numpy 1.6.0 Further information
numexpr 1.4.2 Further information
hdf5 1.8.7 Further information
Cython 0.14.1 Further information
Python Tables (tables) 2.2.1 Further information
FastX Toolkit 0.0.13 Further information

Available datasets

Genome Downloaded Blast Database BWA Index Bowtie Index PerM Index Sam Index SRMA Dict
hg19 (by chromosome) Yes Yes No Yes Yes Yes Yes
Mouse (mm9) Yes Yes No Yes Yes Yes Yes
Vaccinia Western Reserve Yes Yes Yes Yes Yes Yes Yes
Mycoplasma pneumonniae (M129) Yes Yes No Yes Yes Yes Yes
Mycoplasma pneumonniae (FH) Yes Yes No Yes Yes Yes Yes
Chromosome 11 Mouse Contigs Yes Yes No Yes Yes Yes Yes

Public instance

A public instance of Galaxy maintained by Penn State University is at


In order to facilitate interaction among UAB Galaxy users, share experience, and provide peer-support we have established a galaxy-users group. To join this group and participate in email discussions please subscribe to the galaxy-user group. On-line archives of these discussions are available here. Please note, the email discussions are a public forum. You are advised to only post information you are authorized to share and comfortable with being public.