20 lines
1.3 KiB
Shell
Executable file
20 lines
1.3 KiB
Shell
Executable file
#!/bin/bash -x
|
|
#
|
|
# redundant input per subject
|
|
|
|
subid=$1
|
|
|
|
# define DSLOCKFILE, DATALAD & GIT ENV for participant_job
|
|
export DSLOCKFILE=/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005529-mriqc/.SLURM_datalad_lock DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__102container="ria+file:///p/data1/inm7/containerstores#{id}" DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__200ds005529=/p/scratch/icei-hbp-00000000004/STAGE/OpenNeuro/ds005529.git GIT_AUTHOR_NAME=$(git config user.name) GIT_AUTHOR_EMAIL=$(git config user.email) JOBID=ds005529_${subid:4}.${SLURM_JOB_ID} REPRONIM_USE_DUCT=1
|
|
|
|
# use subject specific folder
|
|
mkdir /local/nvme/${JOBID}
|
|
cd /local/nvme/${JOBID}
|
|
|
|
# run things
|
|
/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005529-mriqc/code/participant_job ria+file:///p/project1/icei-hbp-00000000004/ria-qcworkflow/inputstore#cfcdf924-8b30-4ba8-91f5-323d14cb572d https://hub.trr379.de/f.hoffstaedter/ds005529-mriqc ${subid} >/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005529-mriqc/logs/${JOBID}.out 2>/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005529-mriqc/logs/${JOBID}.err
|
|
|
|
cd /local/nvme/
|
|
chmod 777 -R /local/nvme/${JOBID}
|
|
rm -fr /local/nvme/${JOBID}
|
|
|