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toil_examples/source_selection.sh

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+#!/bin/bash
+
+#### UPDATE THESE ####
+
+export TOIL_SLURM_ARGS="--export=ALL --job-name phasediff -p normal -t 4:00:00"
+SING_BIND="/project,/project/lofarvwf/Software,/project/lofarvwf/Share,/project/lofarvwf/Public,/home/lofarvwf-jdejong"
+VLBI_SCRIPTS="/project/lofarvwf/Software/vlbi/scripts/"
+
+CWL_WORKFLOW=/project/lofarvwf/Software/lofar_helpers/source_selection/pre_selection/ddcal_pre_selection.cwl
+YAML=input.yaml
+VENV=/home/lofarvwf-jdejong/venv
+
+######################
+
+# set up singularity
+SIMG=vlbi-cwl.sif
+mkdir -p singularity
+wget https://lofar-webdav.grid.sara.nl/software/shub_mirror/tikk3r/lofar-grid-hpccloud/amd/flocs_v4.5.0_znver2_znver2_aocl4_cuda.sif -O singularity/$SIMG
+mkdir -p singularity/pull
+cp singularity/$SIMG singularity/pull/$SIMG
+
+CONTAINERSTR=$(singularity --version)
+if [[ "$CONTAINERSTR" == *"apptainer"* ]]; then
+  export APPTAINER_CACHEDIR=$PWD/singularity
+  export APPTAINER_TMPDIR=$APPTAINER_CACHEDIR/tmp
+  export APPTAINER_PULLDIR=$APPTAINER_CACHEDIR/pull
+  export APPTAINER_BIND=$SING_BIND
+  export APPTAINERENV_PYTHONPATH='$VLBI_SCRIPTS:$PYTHONPATH'
+else
+  export SINGULARITY_CACHEDIR=$PWD/singularity
+  export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
+  export SINGULARITY_PULLDIR=$SINGULARITY_CACHEDIR/pull
+  export SINGULARITY_BIND=$SING_BIND
+  export SINGULARITYENV_PYTHONPATH='$VLBI_SCRIPTS:$PYTHONPATH'
+fi
+
+export CWL_SINGULARITY_CACHE=$APPTAINER_CACHEDIR
+export TOIL_CHECK_ENV=True
+
+# make folder for running toil
+WORKDIR=$PWD/workdir
+OUTPUT=$PWD/outdir
+JOBSTORE=$PWD/jobstore
+LOGDIR=$PWD/logs
+TMPD=$PWD/tmpdir
+
+mkdir -p ${TMPD}_interm
+mkdir -p $WORKDIR
+mkdir -p $OUTPUT
+mkdir -p $LOGDIR
+
+source ${VENV}/bin/activate
+
+# run toil
+toil-cwl-runner \
+--no-read-only \
+--retryCount 0 \
+--singularity \
+--disableCaching \
+--writeLogsFromAllJobs True \
+--logFile full_log.log \
+--writeLogs ${LOGDIR} \
+--outdir ${OUTPUT} \
+--tmp-outdir-prefix ${TMPD}/ \
+--jobStore ${JOBSTORE} \
+--workDir ${WORKDIR} \
+--coordinationDir ${OUTPUT} \
+--tmpdir-prefix ${TMPD}_interm/ \
+--disableAutoDeployment True \
+--bypass-file-store \
+--preserve-entire-environment \
+--batchSystem slurm \
+${CWL_WORKFLOW} ${YAML}
+
+#--cleanWorkDir never \ --> for testing
+
+deactivate