Linux cluster

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		+	{| align="left" cellpadding="15"
		+	|__TOC__
		+	|}
		+
	[[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]]		[[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]]
	==Administration==		==Administration==
	*Change locale (language)		*Change locale (language)
-	<pre>bash shell:	+	<pre>
		+	# bash
	export LC_ALL=en_GB.ISO8859-1		export LC_ALL=en_GB.ISO8859-1
	export LANG=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
	</pre>		</pre>
		+
	==Parallel computing==		==Parallel computing==
		+	===Examples===
		+	*[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores]
		+	*[http://www.clusterresources.com/products/torque/docs/2.1jobsubmission.shtml qsub examples]
		+	*[http://compbio.korea.ac.kr/wiki/images/c/cb/Parallel_scripts.zip Parallel scripts]
		+	*[http://beowulf.csail.mit.edu/18.337/index.html 18.337/6.338 Parallel Computing @MIT]
		+
	===MEME===		===MEME===
	*[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 a following option
		+	<pre>qsub -q infi</pre>
	*memebatch.csh:		*memebatch.csh:
	<pre>		<pre>
Line 18:		Line 35:
	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		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>		</pre>
-	*[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores]	+	;meme option [http://www.sdsc.edu/~tbailey/MEME-protocol-draft2/protocols.html Current protocols]
-	*[http://www.clusterresources.com/torquedocs21/users/2.1jobsubmission.shtml#nodeExamples qsub node examples]	+	:-evt 0.001 (E-value thershold 0.001)
-	*[http://compbio.korea.ac.kr/wiki/images/c/cb/Parallel_scripts.zip Parallel scripts]	+
	==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)
		+
		+	;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
-	*Assembly packages	+	:ETC
-	**AMOS	+	::realigner
-	**EMBOSS(/usr/local/share/EMBOSS)	+	::SOAPaligner
-	**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===		===Modules===
Line 65:		Line 87:
	**Rpy ( RHOME problem)		**Rpy ( RHOME problem)
	*Perl modules		*Perl modules
		+	**Moose[[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/README]]
		+	**Bioperl[[http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix]]
		+	**Bundle::CPAN
		+	**Module::Build
	==Log book==		==Log book==
	[[Panpyro]]		[[Panpyro]]
		+	==Misc.==
		+	*Open source OS for linux cluster: [http://biobrew.bioinformatics.org/ Biobrew]
		+	*[http://blog.neosgen.net/16 생물정보학자를 위한 클러스터 만들기]
		+	http://image.aladin.co.kr/coveretc/book/coversum/8983794402_1.jpg

---

Latest revision as of 06:02, 1 October 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

meme option Current protocols

-evt 0.001 (E-value thershold 0.001)

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