vbbatch

From VoxBoWiki

vbbatch is a command line tool that allows you to submit a bunch of command lines to the queue. You just need to specify the command line and a list of files to be substituted into the command line (wherever the string FILE appears). For safety, by default vbbatch just shows you the commands. If you're happy with what you see, use the -r flag to make it happen.

Here's the help text:

VoxBo vbbatch (v1.8.5pre8/May  6 2010)
usage:
  vbbatch -c <command> [<file> ...]
flags:
  -c "command"   command line to execute (should be in quotes)
  -p <pri>       set job priority
  -x <str>       use str as your variable string instead of FILE
  -n <str>       use str as your index string instead of IND
  -m <maxjobs>   maximum number of concurrent jobs at full priority
  -r             really run it, don't just show the commands
  -req <req>     add a requirement (you'll know if you need it)
  -i             interactive mode (ask for each file)
  -d <n>         add a bunch of dummy files (see below)
  -sn <seqname>  sequence name visible in queue
  -jn <jobname>  job names visible in queue (can use FILE, IND)
  -f <seq>       flush private sequence
  -a <seq>       append to private sequence
  -s <seq>       submit private sequence
  -e <email>     address for notification, use -- for no email
  --run=<n>      don't queue, run now on n cores
  -h             show help
  -v             show version
notes:
  In your command, the token FILE will be replaced with each file you
  specify.  The token IND will be replaced with an index, starting from 000
  
  maxjobs defaults to 10
  
  The -f, -a, and -s options allow you to build a compound
  batch job in pieces, and then to submit the whole thing as
  one sequence.  Use -f to first flush it (just in case), then
  call vbbatch as you normally would, but use -a to append the
  jobs to your private sequence, and finally use -s to submit
  the whole thing.
  
  The -r flag is there to encourage you to check the generated
  command lines before you really submit.  Run vbbatch without it,
  and if you like what you see, run it again with -r.
  
  The -p flag can take a numeric priority from 0 to 5 or a scheduling
  policy as described in the help to voxq.

  If --run is specified without =n, the default is the total number of
  available cores minus 1 (or 1, if that would be 0).  Note that even
  if you use --run, you still have to include the -r flag to indicate
  you really want to run the jobs, not just see them.

  The -d flag lets you create "dummy" files, with the filenames just
  being the numbers from 0 to n-1.  Usually you would use it with IND,
  not FILE.
examples:
  Run myscript.sh on all your subjects' Anatomy directories:

    vbbatch -c "myscript.sh FILE" study*/sub*/Anatomy -r

  Run myperms.sh 1000 times at low priority, with different output
  files:

    vbbatch -c "myperms.sh results_IND.nii.gz" -d 1000 -r -p xnice