Galaxy
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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
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.
The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.
Using Galaxy / Tutorials
There are numerous general tutorials online at the Penn State public Galaxy site that are worth looking at.
There are also several UAB tutorials on NGS Analysis with Galaxy, created for HPC Boot Camp 2011 and a nice talk by Jeremy Goecks during Research Computing Day 2011.
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 (production galaxy instance)
- $HOME/projects/galaxy/galaxy (personal galaxy instance)
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 $GALAXY/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 $HOME/projects/galaxy/galaxy/tool-data/shared/ucsc/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
Index Creation
Index for Bowtie, BWA and SAM are created in /lustre/project/public_datasets/derived by the tool $GALAXY/scripts/uab/index_genome.bsh. If you need additional types of indices, please update that script. Note: $GALAXY will likely be your personal galaxy: /home/USER/projects/galaxy/galaxy
$GALAXY/scripts/uab/index_genome.bsh sacCer2
Configuration File Update
Follow the detail instructions that Shantanu has posted for creating a git branch for your changes, they can be found here: http://projects.uabgrid.uab.edu/galaxy/wiki/GalaxyDevelopment
Once you branch is prepared, you register the genome as follows:
- add your new dbkey to tool-data/shared/ucsc/builds.txt
- run the script $GALAXY/scripts/uab/register_genome_with_galaxy.bsh to updated the tool-data/*.loc files and copy the .len file.
$GALAXY/scripts/uab/register_genome_with_galaxy.bsh sacCer2
You will then have to do the necessary "git add" and "git commit", etc, and send the patch to Shantanu.
This will be committed and others can add to it to update blast databases, perM, and other indices as needed.
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. It is best to send a patch or set up your directory so he can pull from it.
Available datasets
| Genome | Downloaded | Blast Database | BWA Index | Bowtie Index | PerM Index | Sam Index | SRMA Dict |
|---|---|---|---|---|---|---|---|
| hg19 (by chromosome) | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Mouse (mm9) | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Vaccinia Western Reserve | Yes | No | Yes | Yes | Yes | Yes | Yes |
| Mycoplasma pneumonniae (M129) | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Mycoplasma pneumonniae (FH) | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Chromosome 11 Mouse Contigs | Yes | No | Yes | Yes | Yes | Yes | Yes |
| S. cerevisae (sacCer2) | Yes | No | Yes | Yes | No | Yes | Yes |
| C. elegans (ce6 and WS226) | Yes | No | Yes | Yes | No | Yes | Yes |
| Tree Shrew 62 | Yes | No | Yes | Yes | No | 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-user 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. In addition to the galaxy-user mailing list, we have a galaxy-annce mailing list for UAB's galaxy instance related announcements. The galaxy-annce is a low volume mailing list for announcing service status and system updates etc. 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.