processing-workflow-tutorial/code/call.job

#!/bin/bash -x
#
# redundant input per subject

subid=$1

# define DSLOCKFILE, DATALAD & GIT ENV for participant_job
export DSLOCKFILE=/data/group/psyinf/ukb_workflow_template/forrest/.SLURM_datalad_lock DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__101cat=https://github.com/ReproNim/containers.git#{id} GIT_AUTHOR_NAME=$(git config user.name) GIT_AUTHOR_EMAIL=$(git config user.email) JOBID=${subid:4}.${SLURM_JOB_ID} 
# use subject specific folder
mkdir /dev/shm//${JOBID}
cd /dev/shm//${JOBID}

# run things
/data/group/psyinf/ukb_workflow_template/forrest/code/participant_job ria+file:///data/group/psyinf/inputstore#47a9ef9e-9fa0-49cd-873f-c51cc501da96 /data/group/psyinf/outputstore/47a/9ef9e-9fa0-49cd-873f-c51cc501da96 ${subid} >/data/group/psyinf/ukb_workflow_template/forrest/logs/${JOBID}.out 2>/data/group/psyinf/ukb_workflow_template/forrest/logs/${JOBID}.err

cd /dev/shm//
chmod 777 -R /dev/shm//${JOBID}
rm -fr /dev/shm//${JOBID}