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vbbatch -c <command> [<file> ...]
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-c "command" command line to execute (should be in quotes)
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-p <pri> set job priority
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-x <str> use str as your variable string instead of FILE
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-n <str> use str as your index string instead of IND
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-m <maxjobs> maximum number of concurrent jobs at full priority
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-r really run it, don't just show the commands
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-req <req> add a requirement (you'll know if you need it)
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-i interactive mode (ask for each file)
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-d <n> add a bunch of dummy files (see below)
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-sn <seqname> sequence name visible in queue
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-jn <jobname> job names visible in queue (can use FILE, IND)
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-f <seq> flush private sequence
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-a <seq> append to private sequence
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-s <seq> submit private sequence
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-e <email> address for notification, use -- for no email
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--run=<n> don't queue, run now on n cores
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In your command, the token FILE will be replaced with each file you
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specify. The token IND will be replaced with an index, starting from 000
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maxjobs defaults to 10
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The -f, -a, and -s options allow you to build a compound
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batch job in pieces, and then to submit the whole thing as
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one sequence. Use -f to first flush it (just in case), then
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call vbbatch as you normally would, but use -a to append the
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jobs to your private sequence, and finally use -s to submit
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The -r flag is there to encourage you to check the generated
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command lines before you really submit. Run vbbatch without it,
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and if you like what you see, run it again with -r.
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The -p flag can take a numeric priority from 0 to 5 or a scheduling
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policy as described in the help to voxq.
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If --run is specified without =n, the default is the total number of
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available cores minus 1 (or 1, if that would be 0). Note that even
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if you use --run, you still have to include the -r flag to indicate
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you really want to run the jobs, not just see them.
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The -d flag lets you create "dummy" files, with the filenames just
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being the numbers from 0 to n-1. Usually you would use it with IND,
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Run myscript.sh on all your subjects' Anatomy directories:
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vbbatch -c "myscript.sh FILE" study*/sub*/Anatomy -r
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Run myperms.sh 1000 times at low priority, with different output
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vbbatch -c "myperms.sh results_IND.nii.gz" -d 1000 -r -p xnice
added
removed
munge/vbbatch.hlp
