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

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
  • Moose[[1]]
  • Bioperl[[2]]
  • Bundle::CPAN
  • Module::Build

Log book

Panpyro

Misc.

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