Linux cluster
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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 | mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4 | ||
</pre> | </pre> | ||
+ | ;meme option [http://www.sdsc.edu/~tbailey/MEME-protocol-draft2/protocols.html Current protocols] | ||
+ | :-evt 0.001 (E-value thershold 0.001) | ||
==Programs Installed== | ==Programs Installed== |
Latest revision as of 06:02, 1 October 2011
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Administration
- Change locale (language)
# bash export LC_ALL=en_GB.ISO8859-1 export LANG=en_GB.ISO8859-1 # csh/tcsh setenv LC_ALL en_GB.ISO8859-1 setenv LANG en_GB.ISO8859-1
Parallel computing
Examples
MEME
qsub -v np=4 -l nodes=node1 memebatch.csh
- CPU time error: add a following option
qsub -q infi
- memebatch.csh:
#!/bin/csh #PBS -N memejobtest setenv PATH /usr/local/mpich/bin:$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
- de Bruijn graphs
- comparative
- maq 0.7.1
- ETC
- realigner
- SOAPaligner
Modules
- Python modules
- biopython
- pyrex
- numpy
- Rpy ( RHOME problem)
- Perl modules
Log book
Misc.
- Open source OS for linux cluster: Biobrew
- 생물정보학자를 위한 클러스터 만들기