PrepareJob
From BIOcrunch
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example: | example: | ||
| − | <source lang="bash"> | + | <source lang="bash" line start="1" highlight="4,13,24,25,26" enclose="div"> |
#!/bin/csh | #!/bin/csh | ||
# | # | ||
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# If you want to make it queue now, get rid of the -a option by adding ## before $ | # If you want to make it queue now, get rid of the -a option by adding ## before $ | ||
# If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS] | # If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS] | ||
| − | #$ -a 201407300600 | + | ##$ -a 201407300600 |
# | # | ||
# | # | ||
Revision as of 17:46, 13 July 2014
Always prepare your jobs fir on your local machine and follow for each job some guidelines.
name your job file and your data files in a consistent way job file: myjobfile.sh User: gerhard email: gerhard@recher.de
you may use this as a template for Beast simply change all occurrences of "myjobfile" to your actual project name. also change User and email to your settings.
example:
- #!/bin/csh
- #
- # Which account to be charged cpu time
- #$ -A gerhard
- #
- #
- # If you want to make it queue now, get rid of the -a option by adding ## before $
- # If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
- ##$ -a 201407300600
- #
- #
- # Send mail to these users
- #$ -M gerhard@recher.de
- #
- # Mail at beginning/end/on suspension
- #$ -m bes
- #
- # Export these environmental variables
- #$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
- #
- # The job is located in the current
- # working directory.
- #$ -cwd
- #$ -o myjobfile.out
- #$ -e myjobfile.err
- #
- env >./xenv
- /share/apps/beast180/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
