Galaxy: Difference between revisions

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Some of the older data sets are still located in or under:
Some of the older data sets are still located in or under:
* /lustre/project/galaxy/public_dataset
* /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


=== FASTA File ===
=== FASTA File ===
Download your FASTA file (doing any conversions needed) and place the file in:
Download your FASTA file (doing any conversions needed) and place the file in:
/lustre/project/public_datasets/primary/ORGANISM/ORGANISM.fa
/lustre/project/public_datasets/primary/MY_GENOME/MY_GENOME.fa
 
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 ===
=== Directory Creation (example for sacSer2) ===
* mkdir /lustre/project/public_datasets/primary/sacCer2
* mkdir /lustre/project/public_datasets/primary/sacCer2
* cd /lustre/project/public_datasets/primary/sacCer2
* cd /lustre/project/public_datasets/primary/sacCer2
Line 150: Line 157:
* mkdir bowtie/base
* mkdir bowtie/base
* mkdir bwa
* mkdir bwa
* mkdir perm
* mkdir sam
* mkdir sam


=== Bowtie Indices (Required for tophat too)
=== Bowtie Indices (Required for tophat too)
Copy in the 2 bowtie ind
Copy in the 2 bowtie files from
/lustre/project/public_datasets/derived/sacCer2/bowtie/base
/lustre/project/public_datasets/derived/sacCer2/bowtie/base
* reindex_bowtie_sacCer2.bsh
* submit_index_job
To your /lustre/project/public_datasets/derived/MY_GENOME/bowtie/base directory.
Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run:
./submit_index_job
== BWA Indices ==
Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:
* reindex_sam_sacCer2.bsh
* submit_index_job
To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.
Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run:
./submit_index_job
== Sam and FAIDX indices ==
Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:
* reindex_sam_sacCer2.bsh
* submit_index_job
To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.
Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run:
./submit_index_job


=== Available datasets ===
=== Available datasets ===

Revision as of 17:56, 25 August 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. 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

I describe here setting up a basic genome and include only a description of how to set up 3 critical pieces:

  • bwa
  • bowtie
  • samtools

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

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) Copy in the 2 bowtie files from /lustre/project/public_datasets/derived/sacCer2/bowtie/base

  • reindex_bowtie_sacCer2.bsh
  • submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/bowtie/base directory.

Replace sacCer2 with the name of your genome (MY_GENOME) in both files. Run: ./submit_index_job

BWA Indices

Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:

  • reindex_sam_sacCer2.bsh
  • submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.

Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run: ./submit_index_job

Sam and FAIDX indices

Copy from /lustre/project/public_datasets/derived/sacCer2/sam/:

  • reindex_sam_sacCer2.bsh
  • submit_index_job

To your /lustre/project/public_datasets/derived/MY_GENOME/sam directory.

Replace sacCer2 with the name of your organism (MY_GENOME) in both files. Run: ./submit_index_job


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.

References