-- HangiKim - 31 Jul 2009

ui-1: /var/www/html/tutorial

scenario 1 (SW:wget, DATA:wget)

First section, to test NBP-search-09.sh script on local machine.

$wget http://ui-1/tutorial/NBP-search-09.sh

$chmod +x NBP-search-09.sh

single job on Local :

$wget http://ui-1/tutorial/NBP-search-09.py

$ganga NBP-search-09.py

Second section, to run massive production script for ganga

$wget http://ui-1/tutorial/cern_run_production.py

To do this, you need list.txt file gene database & seqence list file : http://ui-1/tutorial/list.txt

$wget http://ui-1/tutorial/list.txt

note: you can also change max number defined in cern_run_production.py now, max number is 2.

$ganga cern_run_production.py

This script submits 2 sub-jobs.

Last section, to run diane script.

NBPsearch script for DIANA: http://ui-1/tutorial/NBPsearch.run

$wget http://ui-1/tutorial/NBPsearch.run

NBPsearch.run also needs two files.

NBPsearch shell script (submitted to the worker): http://ui-1/tutorial/NBP-search-09.sh need list.txt file : http://ui-1/tutorial/list.txt ( import: put list.txt you home directory /home/your_id )

to start DIANE server

$diane-run NBPsearch.run

and then, submit worker on LCG Grid.

$ganga LCGSubmitter.py --diane-download-url=http://ui-1/diane/packages --diane-worker-number 2

scenario 2 (SW:SW_DIR, DATA:wget)

First section, to test NBP-search-09-SW_DIR.sh script on LCG.

$wget http://ui-1/tutorial/NBP-search-09-SW_DIR.sh

$chmod +x NBP-search-09-SW_DIR.sh

single job on LCG :

$wget http://ui-1/tutorial/NBP-search-09-SW_DIR.py

$ganga NBP-search-09-SW_DIR.py

Second section, to run massive production script for ganga

$wget http://ui-1/tutorial/cern_run_production-SW_DIR.py

To do this, you also need list.txt file gene database & seqence list file : http://ui-1/tutorial/list.txt

$wget http://ui-1/tutorial/list.txt

note: you can also change max number defined in cern_run_production-SW_DIR.py now, max number is 2.

$ganga cern_run_production-SW_DIR.py

This script submits 2 sub-jobs.

Last section, to run diane script.

NBPsearch script for DIANA: http://ui-1/tutorial/NBPsearch-SW_DIR.run

$wget http://ui-1/tutorial/NBPsearch-SW_DIR.run

NBPsearch-SW_DIR.run also needs two files.

NBPsearch shell script (submitted to the worker): http://ui-1/tutorial/NBP-search-09-SW_DIR.sh need list.txt file : http://ui-1/tutorial/list.txt ( import: put list.txt you home directory /home/your_id )

to start DIANE server

$diane-run NBPsearch-SW_DIR.run

and then, submit worker on LCG Grid.

$ganga LCGSubmitter.py --diane-download-url=http://ui-1/diane/packages --diane-worker-number 2

scenario 3 (SW:SW_DIR, DATA:Storage Element)

First section, to test NBP-search-09-SW_DIR-SE.sh script on LCG.

$wget http://ui-1/tutorial/NBP-search-09-SW_DIR-SE.sh

$chmod +x NBP-search-09-SW_DIR-SE.sh

single job LCG :

$wget http://ui-1/tutorial/NBP-search-09-SW_DIR-SE.py

$ganga NBP-search-09-SW_DIR-SE.py

Second section, to run massive production script for ganga

$wget http://ui-1/tutorial/cern_run_production-SW_DIR-SE.py

To do this, you also need list.txt file gene database & seqence list file : http://ui-1/tutorial/list.txt

$wget http://ui-1/tutorial/list.txt

note: you can also change max number defined in cern_run_production-SW_DIR-SE.py now, max number is 2.

$ganga cern_run_production-SW_DIR-SE.py

This script submits 2 sub-jobs.

Last section, to run diane script.

NBPsearch script for DIANA: http://ui-1/tutorial/NBPsearch-SW_DIR-SE.run

$wget http://ui-1/tutorial/NBPsearch-SW_DIR-SE.run

NBPsearch-SW_DIR-SE.run also needs two files.

NBPsearch shell script (submitted to the worker): http://ui-1/tutorial/NBP-search-09-SW_DIR-SE.sh need list.txt file : http://ui-1/tutorial/list.txt ( import: put list.txt you home directory /home/your_id )

to start DIANE server

$diane-run NBPsearch-SW_DIR-SE.run

and then, submit worker on LCG Grid.

$ganga LCGSubmitter.py --diane-download-url=http://ui-1/diane/packages --diane-worker-number 2


.bashrc:

export LFC_HOST=central-1.grid.seed

alias cinit='voms-proxy-init --voms gridseed'
alias diane='source /opt/diane/env.sh'
alias vinfo='voms-proxy-info --all'
alias info='lcg-infosites --vo gridseed'

[hangi@ui-1 ~]$ lfc-ls /grid/gridseed/
SmallSeq
genomeLibTutorial
ncbi_human_genome
test.txt
ts_database
ts_samples
tyanko

/var/www/html/data/seq =  /grid/gridseed/SmallSeq
/var/www/html/data/hs_ref_chr1.fa.gz = /grid/gridseed/ncbi_human_genome/hs_ref_chr1.fa.gz

source code related to the tutorial: /var/www/html/tutorial/

BLAST software: /var/www/html/software/app-release.tgz

reference site: http://grid.cyfronet.pl/szepieniec/bg2school/doku.php

thanks to Jakub Moscicki, Tomasz Szepieniec, Tadeusz.

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Topic revision: r10 - 2009-08-12 - HangiKim
 
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