41 lines
1.7 KiB
Shell
Executable file
41 lines
1.7 KiB
Shell
Executable file
#!/bin/bash
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subid="$1"
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executable=$(pwd)/code/participant_job
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# the job expects these environment variables for labeling and synchronization
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# - JOBID: subject AND process specific ID to make a branch name from
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# (must be unique across all (even multiple) submissions)
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# including the cluster ID will enable sorting multiple computing attempts
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# - DSLOCKFILE: lock (must be accessible from all compute jobs) to synchronize
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# write access to the output dataset
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# - DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__...:
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# (additional) locations for datalad to locate relevant subdatasets, in case
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# a configured URL is outdated
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# - GIT_AUTHOR_...: Identity information used to save dataset changes in compute
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# jobs
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export JOBID=${subid} \
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DSLOCKFILE=$(pwd)/.condor_datalad_lock \
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GIT_AUTHOR_NAME='Felix Hoffstaedter' \
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GIT_AUTHOR_EMAIL='f.hoffstaedter@fz-juelich.de' \
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REPRONIM_USE_DUCT=1
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# essential args for "participant_job"
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# 1: where to clone the analysis dataset
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# 2: location to push the result git branch to. The "ria+" prefix is stripped.
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# 3: ID of the subject to process
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arguments="ria+file:///p/project1/icei-hbp-00000000004/ria-qcworkflow/inputstore#58134492-e50f-413f-a32c-a5c22cdb8719 \
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https://hub.trr379.de/f.hoffstaedter/ds005386-mriqc \
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${subid} \
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"
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mkdir -p /local/nvme/tmp_${subid:4}
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cd /local/nvme/tmp_${subid:4}
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${executable} ${arguments} \
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> /p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005386-mriqc/logs/${subid}.out \
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2> /p/project1/icei-hbp-00000000004/QCworkflow/openneuro-qc/openneuro-mriqc_local/ds005386-mriqc/logs/${subid}.err
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chmod +w -R /local/nvme/tmp_${subid:4} && rm -rf /local/nvme/tmp_${subid:4}
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