Linux cluster
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[[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]] | [[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]] | ||
==Administration== | ==Administration== | ||
*Change locale (language) | *Change locale (language) | ||
- | <pre>bash | + | <pre> |
+ | # bash | ||
export LC_ALL=en_GB.ISO8859-1 | export LC_ALL=en_GB.ISO8859-1 | ||
export LANG=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 | ||
</pre> | </pre> | ||
+ | |||
==Parallel computing== | ==Parallel computing== | ||
===Examples=== | ===Examples=== | ||
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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== | ||
===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 | |
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===Modules=== | ===Modules=== | ||
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*Open source OS for linux cluster: [http://biobrew.bioinformatics.org/ Biobrew] | *Open source OS for linux cluster: [http://biobrew.bioinformatics.org/ Biobrew] | ||
*[http://blog.neosgen.net/16 생물정보학자를 위한 클러스터 만들기] | *[http://blog.neosgen.net/16 생물정보학자를 위한 클러스터 만들기] | ||
- | http://image. | + | http://image.aladin.co.kr/coveretc/book/coversum/8983794402_1.jpg |
Latest revision as of 06:02, 1 October 2011
|
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