Linux cluster
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==Programs Installed== | ==Programs Installed== | ||
===Bin directory (/home/tools)=== | ===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=== | ===Modules=== |
Revision as of 06:49, 21 March 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
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