Linux cluster

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Revision as of 14:55, 29 July 2009 (view source) Igchoi (Talk | contribs) (→MEME) ← Older edit		Revision as of 14:56, 29 July 2009 (view source) Igchoi (Talk | contribs) (→MEME) Newer edit →
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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	+	*memebatch
	<pre>		<pre>
	#!/bin/csh		#!/bin/csh

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Revision as of 14:56, 29 July 2009

Contents 1 Parallel computing 1.1 MEME 2 Programs Installed 2.1 Bin directory (/home/tools) 2.2 Modules

Parallel computing

MEME

• parallel 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

• assigning nodes & cores
• qsub node examples
• Parallel scripts

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

1. de Bruijn graphs
   1. velvet
   2. abyss 1.0.5
2. suffix tree-based approach
   1. QSRA
   2. SSAKE
3. overlap-layout-consensus
   1. edena
4. ??
   1. 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