Linux cluster

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Revision as of 06:51, 19 March 2010 (view source) Igchoi (Talk | contribs) (→MEME) ← Older edit		Revision as of 08:02, 19 March 2010 (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>
-	*CPU time error: add following option	+	*CPU time error: add a following option
	<pre>qsub -q infi</pre>		<pre>qsub -q infi</pre>
	*memebatch.csh:		*memebatch.csh:

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Revision as of 08:02, 19 March 2010

Contents 1 Administration 2 Parallel computing 2.1 MEME 3 Programs Installed 3.1 Bin directory (/home/tools) 3.2 Modules 4 Log book

Administration

• Change locale (language)

bash shell:
export LC_ALL=en_GB.ISO8859-1
export LANG=en_GB.ISO8859-1

Parallel computing

MEME

• parallel meme

qsub -v np=4 -l nodes=node1 memebatch.csh

• CPU time error: add a following option

qsub -q infi

• memebatch.csh:

#!/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
    • RMySQL
    • DBI

• 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
  • ETC
    • realigner
    • SOAPaligner

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• Sequence analysis
  • manatee(requir setting DIR)
  • iprscan
  • BLAST

Modules

• Python modules
  • biopython
  • pyrex
  • numpy
  • Rpy ( RHOME problem)
• Perl modules
  • Moose[[1]]
  • Bioperl[[2]]
  • Bundle::CPAN
  • Module::Build

Log book

Panpyro