Linux cluster
From CSBLwiki
(Difference between revisions)
Line 66: | Line 66: | ||
*Perl modules | *Perl modules | ||
**Moose | **Moose | ||
- | **Bioperl | + | **Bioperl[[http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix]] |
+ | **Bundle::CPAN | ||
+ | **Module::Build | ||
==Log book== | ==Log book== | ||
[[Panpyro]] | [[Panpyro]] |
Revision as of 06:10, 12 October 2009
Contents |
Administration
- Change locale (language)
bash shell: export LC_ALL=en_GB.ISO8859-1 export LANG=en_GB.ISO8859-1
Parallel computing
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
Programs Installed
Bin directory (/home/tools)
- Statistical Packages
- R-2.8.1
- RMySQL
- DBI
- R-2.8.1
- 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
- de Bruijn graphs
- 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
- Bioperl[[1]]
- Bundle::CPAN
- Module::Build