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biac:cluster:examples:bet
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biac:cluster:examples:bet [2017/07/31 18:11] cmp12 |
biac:cluster:examples:bet [2023/02/23 18:43] |
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| - | ====== BET Example Cluster Script ====== | ||
| - | The script below will run FSL's BET (brain extraction tool) on any MR image, provided it is in an image format that FSL can read. | ||
| - | |||
| - | ===== qsub_fsl_bet ===== | ||
| - | Example usage: | ||
| - | < | ||
| - | [user@head ~]$ qsub -v EXPERIMENT=Dummy.01 qsub_fsl_bet EXPERIMENT/ | ||
| - | | ||
| - | </ | ||
| - | |||
| - | Copy and edit code below: | ||
| - | <code bash> | ||
| - | #!/bin/sh | ||
| - | |||
| - | # This is a BIAC template script for jobs on the cluster | ||
| - | # You have to provide the Experiment on command line | ||
| - | # when you submit the job the cluster. | ||
| - | # | ||
| - | # > qsub -v EXPERIMENT=Dummy.01 | ||
| - | # | ||
| - | # There are 2 USER sections | ||
| - | # 1. USER DIRECTIVE: If you want mail notifications when | ||
| - | # your job is completed or fails you need to set the | ||
| - | # | ||
| - | # | ||
| - | # 2. USER SCRIPT: Add the user script in this section. | ||
| - | # | ||
| - | # | ||
| - | # eg: $EXPERIMENT/ | ||
| - | # By default all terminal output is routed to the " Analysis " | ||
| - | # | ||
| - | # To change this path, set the OUTDIR variable in this section | ||
| - | # to another location under your experiment folder | ||
| - | # eg: OUTDIR=$EXPERIMENT/ | ||
| - | # By default on successful completion the job will return 0 | ||
| - | # If you need to set another return code, set the RETURNCODE | ||
| - | # | ||
| - | # | ||
| - | # eg: RETURNCODE=110 | ||
| - | # | ||
| - | # | ||
| - | # The remaining sections are setup related and don't require | ||
| - | # modifications for most scripts. They are critical for access | ||
| - | # to your data | ||
| - | |||
| - | # --- BEGIN GLOBAL DIRECTIVE -- | ||
| - | #$ -S /bin/sh | ||
| - | #$ -o $HOME/ | ||
| - | #$ -e $HOME/ | ||
| - | #$ -m ea | ||
| - | # -- END GLOBAL DIRECTIVE -- | ||
| - | |||
| - | # -- BEGIN PRE-USER -- | ||
| - | #Name of experiment whose data you want to access | ||
| - | EXPERIMENT=${EXPERIMENT:?" | ||
| - | |||
| - | EXPERIMENT=`biacmount $EXPERIMENT` | ||
| - | EXPERIMENT=${EXPERIMENT:?" | ||
| - | |||
| - | if [ $EXPERIMENT = " | ||
| - | then | ||
| - | exit 32 | ||
| - | else | ||
| - | #Timestamp | ||
| - | echo " | ||
| - | # -- END PRE-USER -- | ||
| - | # ********************************************************** | ||
| - | |||
| - | # -- BEGIN USER DIRECTIVE -- | ||
| - | # Send notifications to the following address | ||
| - | #$ -M user@somewhere.edu | ||
| - | |||
| - | # -- END USER DIRECTIVE -- | ||
| - | |||
| - | # -- BEGIN USER SCRIPT -- | ||
| - | # User script goes here | ||
| - | |||
| - | # Need to input global EXPERIMENT, and inputs INFILE, OUTDIR, and OUTPRE | ||
| - | # INFILE is the file path and name of the file to process | ||
| - | # OUTDIR is where the output folder will go | ||
| - | # OUTPRE is the output prefix of the file | ||
| - | # Example: | ||
| - | # EXPERIMENT/ | ||
| - | # EXPERIMENT/ | ||
| - | |||
| - | INFILE=$1 | ||
| - | OUTDIR=$2 | ||
| - | OUTPRE=$3 | ||
| - | |||
| - | # In this bash syntax, the preceding string " | ||
| - | # from the string $INFILE. | ||
| - | # Example: | ||
| - | # If INFILE = EXPERIMENT/ | ||
| - | # running ${INFILE# | ||
| - | # / | ||
| - | |||
| - | INFILE=${EXPERIMENT}${INFILE# | ||
| - | OUTDIR=${EXPERIMENT}${OUTDIR# | ||
| - | BETVALUE=0.05 | ||
| - | |||
| - | mkdir -p $OUTDIR | ||
| - | echo "bet $INFILE $OUTDIR/ | ||
| - | bet $INFILE $OUTDIR/ | ||
| - | |||
| - | |||
| - | # -- END USER SCRIPT -- # | ||
| - | |||
| - | # ********************************************************** | ||
| - | # -- BEGIN POST-USER -- | ||
| - | echo " | ||
| - | OUTDIR=${OUTDIR: | ||
| - | mv $HOME/ | ||
| - | RETURNCODE=${RETURNCODE: | ||
| - | exit $RETURNCODE | ||
| - | fi | ||
| - | # -- END POST USER-- | ||
| - | |||
| - | </ | ||
biac/cluster/examples/bet.txt · Last modified: 2023/02/23 18:43 (external edit)
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