Linux cluster

From CSBLwiki

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
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