Linux cluster

From CSBLwiki

Contents 1 Parallel computing 1.1 MEME 2 Programs Installed 2.1 Bin directory (/home/tools) 2.2 Modules

Parallel computing

MEME

• parallel meme
• assigning nodes & cores
• qsub node examples
• Parallel scripts

Programs Installed

Bin directory (/home/tools)

• Statistical Packages
  • R-2.8.1
• 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