Linux cluster
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- | [[image:panpyro.jpg|thumb|100px| | + | {| align="left" cellpadding="15" |
+ | |__TOC__ | ||
+ | |} | ||
+ | |||
+ | [[image:panpyro.jpg|thumb|100px|right|panpyro 파이숭이]] | ||
+ | ==Administration== | ||
+ | *Change locale (language) | ||
+ | <pre> | ||
+ | # 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 | ||
+ | </pre> | ||
+ | |||
+ | ==Parallel computing== | ||
+ | ===Examples=== | ||
+ | *[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | ||
+ | *[http://www.clusterresources.com/products/torque/docs/2.1jobsubmission.shtml qsub examples] | ||
+ | *[http://compbio.korea.ac.kr/wiki/images/c/cb/Parallel_scripts.zip Parallel scripts] | ||
+ | *[http://beowulf.csail.mit.edu/18.337/index.html 18.337/6.338 Parallel Computing @MIT] | ||
+ | |||
+ | ===MEME=== | ||
+ | *[http://biowulf.nih.gov/apps/meme.html parallel meme] | ||
+ | <pre>qsub -v np=4 -l nodes=node1 memebatch.csh</pre> | ||
+ | *CPU time error: add a following option | ||
+ | <pre>qsub -q infi</pre> | ||
+ | *memebatch.csh: | ||
+ | <pre> | ||
+ | #!/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 | ||
+ | </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 | ||
+ | |||
===Modules=== | ===Modules=== | ||
*Python modules | *Python modules | ||
+ | **biopython | ||
+ | **pyrex | ||
+ | **numpy | ||
+ | **Rpy ( RHOME problem) | ||
*Perl modules | *Perl modules | ||
+ | **Moose[[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/README]] | ||
+ | **Bioperl[[http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix]] | ||
+ | **Bundle::CPAN | ||
+ | **Module::Build | ||
+ | |||
+ | ==Log book== | ||
+ | [[Panpyro]] | ||
+ | ==Misc.== | ||
+ | *Open source OS for linux cluster: [http://biobrew.bioinformatics.org/ Biobrew] | ||
+ | *[http://blog.neosgen.net/16 생물정보학자를 위한 클러스터 만들기] | ||
+ | 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