Linux cluster
From CSBLwiki
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*[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> | <pre>qsub -v np=4 -l nodes=node1 memebatch.csh</pre> | ||
| + | **memebatch | ||
| + | <pre> | ||
| + | #!/bin/csh | ||
| + | #PBS -N memejobtest | ||
| + | setenv PATH /usr/local/mpich/bin:$PATH | ||
| + | cd /home/users/igchoi/exp | ||
| + | mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4 | ||
| + | </pre> | ||
*[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | *[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | ||
*[http://www.clusterresources.com/torquedocs21/users/2.1jobsubmission.shtml#nodeExamples qsub node examples] | *[http://www.clusterresources.com/torquedocs21/users/2.1jobsubmission.shtml#nodeExamples qsub node examples] | ||
Revision as of 14:55, 29 July 2009
Contents |
Parallel computing
MEME
qsub -v np=4 -l nodes=node1 memebatch.csh
- memebatch
#!/bin/csh #PBS -N memejobtest setenv PATH /usr/local/mpich/bin:$PATH cd /home/users/igchoi/exp mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4
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
