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.
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 https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed. However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.
Available Tools
Following is a short list highlighting some of the important tools available:
| Software | Version | Information |
|---|---|---|
| bwa | 0.5.9-r26 | Align genomic short reads to a reference genome |
| bowtie | 0.12.7 | Align genomic short reads to a reference genome |
| samtools | 0.1.12a | Alignment (SAM/BAM file) manipulations |
| velvet | 1.1.03 | Denovo Assembly |
| Top Hat | 1.4.0 | Align transcriptome short reads to a reference genome |
| Cuff Links | 1.3.0 | Reconstruct and quantify transcript levels from tophat alignments. |
| EMBOSS | 6.3.1 | European Molecular Biology Open Software Suite - sequence manipulation and format conversion |
Installed Genome Indexes
You can always use your own genome by uploading the .fasta into your history, but alignments against installed (pre-indexed) genomes run much more quickly. If you need an additional genome installed, please contact [1].
| dbkey | Genome | Accessions |
|---|---|---|
| mm9 | Mouse July 2007 (NCBI37/mm9) (mm9) | |
| mm10 | Mouse Dec. 2011 (GRCm38/mm10) (mm10) | |
| hg18 | Human Mar. 2006 (NCBI36/hg18) (hg18) | |
| hg19 | Human Feb. 2009 (GRCh37/hg19) (hg19) | |
| sacCer2 | S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) | |
| sacCer3 | S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) | |
| ce10 | C. elegans Oct. 2010 (WS220/ce10) (ce10) | |
| rn4 | Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) | |
| rn5 | Rat Mar. 2012 (RGSC 5.0/rn5) (rn5) | |
| danRer7 | Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7) | |
| eschColi_APEC_O1 | Escherichia coli APEC O1 | chr=5082025 |
| eschColi_CFT073 | Escherichia coli CFT073 | chr=5231428 |
| eschColi_EC4115 | Escherichia coli EC4115 | chr=5572075,plasmid_pO157=94644,plasmid_pEC4115=37452 |
| eschColi_K12 | Escherichia coli K12 | chr=4639675 |
| eschColi_EDL993 | Escherichia coli O157:H7 EDL933 | NC_007414=92077,NC_002655=5528445 |
| eschColi_O157H7 | Escherichia coli O157:H7 EDL933 | NC_007414=92077,NC_002655=5528445 |
| eschColi_TW14359 | Escherichia coli TW14359 | chr=5528136,plasmid_pO157=94601 |
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.