Galaxy: Difference between revisions

From Cheaha
Jump to navigation Jump to search
(Removed previous content; Started with user oriented documentation)
Line 2: Line 2:


= Overview =
= Overview =
[http://bitbucket.org/galaxy/galaxy-central/wiki/Home Galaxy] is an easy-to-use, open-source, scalable framework for tool and data integration. Galaxy provides access to tools (mainly comparative genomics) through an interface (e.g., a web-based interface). The [http://bitbucket.org/galaxy/galaxy-central/wiki/ImplementationInfo Galaxy framework] is implemented in the Python programming language.  
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 [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/  UABgrid]. Documentation on the UAB installation can be found on the [http://docs.uabgrid.uab.edu/wiki/Galaxy UAB Galaxy wiki].


= Galaxy@UAB =
= Galaxy@UAB =

Revision as of 13:44, 27 May 2011

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. We are using Galaxy revision 50e249442c5a on campus installation.

Hardware

Behind the scenes the Galaxy server at UAB is powered by Cheaha cluster.

Available Tools

Software Version Information
bwa 0.5.9 Further information
bowtie 0.12.7
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

Available datasets

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 UAB IT Research Computing has 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