Galaxy
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ 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
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. 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
FASTA File
Download your FASTA file (doing any conversions needed) and place the file in: /lustre/project/public_datasets/primary/ORGANISM/ORGANISM.fa
Directory Creation
- 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 perm
- mkdir sam
=== Bowtie Indices (Required for tophat too) Copy in the 2 bowtie ind /lustre/project/public_datasets/derived/sacCer2/bowtie/base
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.