20 lines
1.3 KiB
Shell
Executable file
20 lines
1.3 KiB
Shell
Executable file
#!/bin/bash -x
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#
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# redundant input per subject
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subid=$1
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# define DSLOCKFILE, DATALAD & GIT ENV for participant_job
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export DSLOCKFILE=/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005573-mriqc/.SLURM_datalad_lock DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__102container="ria+file:///p/data1/inm7/containerstores#{id}" DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__200ds005573=/p/scratch/icei-hbp-00000000004/STAGE/OpenNeuro/ds005573.git GIT_AUTHOR_NAME=$(git config user.name) GIT_AUTHOR_EMAIL=$(git config user.email) JOBID=ds005573_${subid:4}.${SLURM_JOB_ID} REPRONIM_USE_DUCT=1
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# use subject specific folder
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mkdir /local/nvme/${JOBID}
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cd /local/nvme/${JOBID}
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# run things
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/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005573-mriqc/code/participant_job ria+file:///p/project1/icei-hbp-00000000004/ria-qcworkflow/inputstore#3fc6459a-db1f-4a5e-9602-e3e9acb3c3a2 https://hub.trr379.de/f.hoffstaedter/ds005573-mriqc ${subid} >/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005573-mriqc/logs/${JOBID}.out 2>/p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005573-mriqc/logs/${JOBID}.err
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cd /local/nvme/
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chmod 777 -R /local/nvme/${JOBID}
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rm -fr /local/nvme/${JOBID}
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