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Revision as of 01:50, 30 July 2009 (view source) Igchoi (Talk | contribs) (→MEME) ← Older edit		Revision as of 01:49, 26 August 2009 (view source) Igchoi (Talk | contribs) Newer edit →
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	[[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]]		[[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]]
		+	==Administration==
		+	*Change locale (language)
		+	<pre>bash shell:
		+	export LC_ALL=en_GB.ISO8859-1
		+	export LANG=en_GB.ISO8859-1
		+	</pre>
	==Parallel computing==		==Parallel computing==
	===MEME===		===MEME===
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	===Bin directory (/home/tools)===		===Bin directory (/home/tools)===
	*Statistical Packages		*Statistical Packages
-	**R-2.8.1	+	**R-2.8.1
-	*assembly packages	+	***RMySQL
-	**amos	+	***DBI
		+
		+	*Assembly packages
		+	**AMOS
	**EMBOSS(/usr/local/share/EMBOSS)		**EMBOSS(/usr/local/share/EMBOSS)
	**EULER ( ?? )		**EULER ( ?? )
-		+	**''ab initio'' assembly
-	*ab initio assembly	+	***ARACHNE 3.2
-	**ARACHNE 3.2	+	***WGS
-	**WGS	+	**''de novo''
-		+
-	*de novo	+
	#de Bruijn graphs		#de Bruijn graphs
	##velvet		##velvet
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	#??		#??
	##SHARCGS		##SHARCGS
-		+	**comparative
-	*comparative	+	***maq 0.7.1
-	**maq 0.7.1	+

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Revision as of 01:49, 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

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