Linux cluster

From CSBLwiki

Revision as of 03:49, 21 August 2010 (view source) Igchoi (Talk | contribs) ← Older edit		Revision as of 06:49, 21 March 2011 (view source) Igchoi (Talk | contribs) (→Bin directory (/home/tools)) Newer edit →
Line 38:		Line 38:
	==Programs Installed==		==Programs Installed==
	===Bin directory (/home/tools)===		===Bin directory (/home/tools)===
-	*Statistical Packages	+	;Sequence analysis
-	**R-2.8.1	+	:MEME (4.6.0) updated 3/21/2011
-	***RMySQL	+	:iprscan
-	***DBI	+	:[[BLAST]]
		+	:EMBOSS(/usr/local/share/EMBOSS)
-	*Assembly packages	+	;Annotation
-	**AMOS	+	:manatee(requir setting DIR)
-	**EMBOSS(/usr/local/share/EMBOSS)	+
-	**EULER ( ?? )	+	;Statistical Packages
-	**''ab initio'' assembly	+	:R-2.8.1
-	***ARACHNE 3.2	+	::RMySQL
-	***WGS	+	::DBI
-	**''de novo''	+
-	***de Bruijn graphs	+	;Assembly packages
-	****velvet	+	:AMOS
-	****abyss 1.0.5	+	:EULER ( ?? )
-	***suffix tree-based approach	+	:''ab initio'' assembly
-	****QSRA	+	::ARACHNE 3.2
-	****SSAKE	+	::WGS
-	***overlap-layout-consensus	+
-	****edena	+	:''de novo''
-	***??	+	::de Bruijn graphs
-	****SHARCGS	+	:::velvet
-	**comparative	+	:::abyss 1.0.5
-	***maq 0.7.1	+	::suffix tree-based approach
-	**ETC	+	:::QSRA
-	***realigner	+	:::SSAKE
-	***SOAPaligner	+	::overlap-layout-consensus
-	----	+	:::edena
-	*Sequence analysis	+	:::??
-	**manatee(requir setting DIR)	+	:::SHARCGS
-	**iprscan	+
-	**[[BLAST]]	+	:comparative
		+	::maq 0.7.1
		+
		+	:ETC
		+	::realigner
		+	::SOAPaligner
	===Modules===		===Modules===

---

Revision as of 06:49, 21 March 2011

Contents 1 Administration 2 Parallel computing 2.1 Examples 2.2 MEME 3 Programs Installed 3.1 Bin directory (/home/tools) 3.2 Modules 4 Log book 5 Misc.

Administration

• Change locale (language)

# bash
export LC_ALL=en_GB.ISO8859-1
export LANG=en_GB.ISO8859-1
# csh/tcsh
setenv LC_ALL en_GB.ISO8859-1
setenv LANG en_GB.ISO8859-1

Parallel computing

Examples

• assigning nodes & cores
• qsub examples
• Parallel scripts
• 18.337/6.338 Parallel Computing @MIT

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

Programs Installed

Bin directory (/home/tools)

Sequence analysis

MEME (4.6.0) updated 3/21/2011

iprscan

BLAST

EMBOSS(/usr/local/share/EMBOSS)

Annotation

manatee(requir setting DIR)

Statistical Packages

R-2.8.1

RMySQL

DBI

Assembly packages

AMOS

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

Modules

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

Log book

Panpyro

Misc.

• Open source OS for linux cluster: Biobrew
• 생물정보학자를 위한 클러스터 만들기