Linux cluster

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Revision as of 01:49, 26 August 2009 (view source) Igchoi (Talk | contribs) ← Older edit		Revision as of 01:52, 26 August 2009 (view source) Igchoi (Talk | contribs) (→Bin directory (/home/tools)) Newer edit →
Line 37:		Line 37:
	***WGS		***WGS
	**''de novo''		**''de novo''
-	#de Bruijn graphs	+	***de Bruijn graphs
-	##velvet	+	****velvet
-	##abyss 1.0.5	+	****abyss 1.0.5
-	#suffix tree-based approach	+	***suffix tree-based approach
-	##QSRA	+	****QSRA
-	##SSAKE	+	****SSAKE
-	#overlap-layout-consensus	+	***overlap-layout-consensus
-	##edena	+	****edena
-	#??	+	***??
-	##SHARCGS	+	****SHARCGS
	**comparative		**comparative
	***maq 0.7.1		***maq 0.7.1
-		+	**ETC
-		+	***realigner
-	*realigner	+	***SOAPaligner
-	*SOAPaligner	+	----
-		+	*Sequence analysis
-	*manatee(requir setting DIR)	+	**manatee(requir setting DIR)
-	*iprscan	+	**iprscan
-	*BLAST	+	**BLAST
	===Modules===		===Modules===

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Revision as of 01:52, 26 August 2009

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

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

• 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

---

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

Modules

• Python modules
  • biopython
  • pyrex
  • numpy
  • Rpy ( RHOME problem)
• Perl modules