Galaxy

Overview

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.

Galaxy@UAB

The UAB Galaxy instance can be accessed at http://galaxy.uabgrid.uab.edu 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).

Hardware

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

Datasets

Adding New Datasets

In order to add a new data set, a series of dependent files must be created and configured on cheaha.uabgrid.uab.edu. The configuration files are located in or under:

• /share/apps/galaxy/galaxy-latest

The dependent files should be located in or under:

• /lustre/project/public_datasets

Some of the older data sets are still located in or under:

• /lustre/project/galaxy/public_dataset

I describe here setting up a basic genome and include only a description of how to set up 3 critical pieces:

• bwa
• bowtie
• samtools

Obviously you will need to have an account on cheaha but you will also need to be in the galaxy-admin group.

FASTA File

Download your FASTA file (doing any conversions needed) and place the file in: /lustre/project/public_datasets/primary/MY_GENOME/MY_GENOME.fa

Make sure the extension is .fa and don't worry if there are multiple files, they can be concatenated together as shown below.

Directory Creation (example for sacSer2)

• mkdir /lustre/project/public_datasets/primary/sacCer2
• cd /lustre/project/public_datasets/primary/sacCer2
• wget http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/chromFa.tar.gz
• tar xzvf chromFa.tar.gz
• cat chr*.fa 2micron.fa > sacCer2.fa
• mkdir /lustre/project/public_datasets/derived/sacCer2
• cd /lustre/project/public_datasets/derived/sacCer2
• mkdir bowtie
• mkdir bowtie/color
• mkdir bowtie/base
• mkdir bwa
• mkdir sam

Bowtie Indices (Required for tophat too)

Copy in the 2 bowtie files from /lustre/project/public_datasets/derived/sacCer2/bowtie/base

• reindex_bowtie_sacCer2.bsh
• submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/bowtie/base directory.

Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run: ./submit_index_job This will run the job on the cluster.

BWA Indices

Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:

• reindex_sam_sacCer2.bsh
• submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.

Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run: ./submit_index_job

This will run the job on cheaha.

Sam and FAIDX indices

Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:

• reindex_sam_sacCer2.bsh
• submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.

Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run: ./submit_index_job

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 http://usegalaxy.org/

Support

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.

References

• Galaxy Wiki
• Galaxy Architecture
• Get Galaxy
• Galaxy Advanced Config