Linux cluster
From CSBLwiki
(Difference between revisions)
(→MEME) |
(→MEME) |
||
Line 3: | Line 3: | ||
===MEME=== | ===MEME=== | ||
*[http://biowulf.nih.gov/apps/meme.html parallel meme] | *[http://biowulf.nih.gov/apps/meme.html parallel meme] | ||
+ | <pre>qsub -v np=4 -l nodes=node1 memebatch.csh</pre> | ||
*[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | *[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | ||
*[http://www.clusterresources.com/torquedocs21/users/2.1jobsubmission.shtml#nodeExamples qsub node examples] | *[http://www.clusterresources.com/torquedocs21/users/2.1jobsubmission.shtml#nodeExamples qsub node examples] |
Revision as of 14:54, 29 July 2009
Contents |
Parallel computing
MEME
qsub -v np=4 -l nodes=node1 memebatch.csh
Programs Installed
Bin directory (/home/tools)
- Statistical Packages
- R-2.8.1
- assembly packages
- amos
- EMBOSS(/usr/local/share/EMBOSS)
- EULER ( ?? )
- ab initio assembly
- ARACHNE 3.2
- WGS
- de novo
- de Bruijn graphs
- velvet
- abyss 1.0.5
- suffix tree-based approach
- QSRA
- SSAKE
- overlap-layout-consensus
- edena
- ??
- SHARCGS
- comparative
- maq 0.7.1
- realigner
- SOAPaligner
- manatee(requir setting DIR)
- iprscan
- BLAST
Modules
- Python modules
- biopython
- pyrex
- numpy
- Rpy ( RHOME problem)
- Perl modules