Galaxy
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The Research Computing Team
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 |
Adding Novel Datasets
Prerequisites
You should have checked out your own galaxy instance and run it from git as described in http://projects.uabgrid.uab.edu/galaxy/wiki/GalaxyDevelopment
Introduction
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
You should following the naming conventions in tool-data/shared/ucsc/builds.txt as shown below.
- sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
For instance, if there is already an entry for your build of S. cerevisiae, then use the dbkey (leftmost column) in builds.txt to name MY_GENOME. In this case it would be sacCer2. In some cases (tree shrew, obscure chimeric mouse genomes you construct yourself) there will be no entry. You will need to edit and create one yourself and update builds.txt.
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)
Switch to your bowtie base directory and copy in the 2 bowtie scripts from another directory, for example sacCer2.
cd /lustre/project/public_datasets/derived/MY_GENOME/bowtie/base cp /lustre/project/public_datasets/derived/sacCer2/bowtie/base/reindex_bowtie_sacCer2.bsh . cp /lustre/project/public_datasets/derived/sacCer2/bowtie/base/submit_index_job .
Find/Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run:
./submit_index_job
This will submit the job on cheaha.
The next step is to add the index to the bowtie configuration files in your personal galaxy project directory. For example to add the treeshrew genome add the line
treeshrew62 treeshrew62 Tree Shrew Build 62 /lustre/project/public_datasets/derived/treeshrew62/bowtie/base/treeshrew6
to the bottom of:
- tool-data/bowtie_indices.loc
and
- tool-data/bowtie_indices_color.loc
BWA Indices
Switch to your bwa directory and copy in the 2 bwa scripts from another directory, for example sacCer2.
cd /lustre/project/public_datasets/derived/MY_GENOME/bwa cp /lustre/project/public_datasets/derived/sacCer2/bwa/reindex_bwa_sacCer2.bsh . cp /lustre/project/public_datasets/derived/sacCer2/bwa/submit_index_job .
Find/Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run:
./submit_index_job
This will submit the job on cheaha.
The next step is to add the index to the bwa configuration files in your personal galaxy project directory. For example to add the treeshrew genome add the line
treeshrew62 treeshrew62 Tree Shrew Build 62 /lustre/project/public_datasets/derived/treeshrew62/bwa/Tupaia_belangeri.TREESHREW.62.dna.nonchromosomal.fa
to the bottom of:
- tool-data/bwa_indices.loc
and
- tool-data/bwa_indices_color.loc
Sam and FAIDX indices
Switch to your sam directory and copy in the 2 bwa scripts from another directory, for example sacCer2.
cd /lustre/project/public_datasets/derived/MY_GENOME/sam cp /lustre/project/public_datasets/derived/sacCer2/sam/reindex_sam_sacCer2.bsh . cp /lustre/project/public_datasets/derived/sacCer2/sam/submit_index_job .
Find/Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run:
./submit_index_job
This will submit the job on cheaha.
The next step is to add the index to the sam configuration files in your personal galaxy project directory. For example to add the treeshrew genome add the line
index treeshrew62 /lustre/project/public_datasets/derived/treeshrew62/sam/Tupaia_belangeri.TREESHREW.62.dna.nonchromosomal.fa
to the bottom of:
- tool-data/sam_fa_indicess.loc
Also add the index to the srma configuration file (again tree shrew example)
treeshrew62 treeshrew62 Tree Shrew Build 62 /lustre/project/public_datasets/derived/treeshrew62/sam/Tupaia_belangeri.TREESHREW.62.dna.nonchromosomal.fa
in the file
- tool-data/srma_index.loc
Final Steps
Log in to your local galaxy and see if you can run your job. If it all works out, contact Shantanu and push the changes to production.
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.