ds003151_ReproVBM/code/process.sub

#!/bin/bash

subject=$1

executable=$(pwd)/code/participant_job

# the job expects these environment variables for labeling and synchronization
# - JOBID: subject AND process specific ID to make a branch name from
#     (must be unique across all (even multiple) submissions)
#     including the cluster ID will enable sorting multiple computing attempts
# - DSLOCKFILE: lock (must be accessible from all compute jobs) to synchronize
#     write access to the output dataset
# - DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__...:
#     (additional) locations for datalad to locate relevant subdatasets, in case
#     a configured URL is outdated
# - GIT_AUTHOR_...: Identity information used to save dataset changes in compute
#     jobs
export JOBID=${subject} \
  DSLOCKFILE=$(pwd)/.condor_datalad_lock \
  GIT_AUTHOR_NAME='Felix Hoffstaedter' \
  GIT_AUTHOR_EMAIL='f.hoffstaedter@fz-juelich.de'

# essential args for "participant_job"
# 1: where to clone the analysis dataset
# 2: location to push the result git branch to. The "ria+" prefix is stripped.
# 3: ID of the subject to process
arguments="ria+file:///data/project/cat_preprocessed/inputstore#37bffb24-5e86-4bee-80f3-835e5ae27a87 \
  /data/project/infrasound/dataladstore/37b/ffb24-5e86-4bee-80f3-835e5ae27a87 \
  ${subject} \
  "

mkdir -p /tmp/tmp_${subject:4}
cd /tmp/tmp_${subject:4}

${executable} ${arguments} \
> /data/project/infrasound/ReproVBM/ds003151_ReproVBM/logs/${subject}.out \
2> /data/project/infrasound/ReproVBM/ds003151_ReproVBM/logs/${subject}.err

chmod 777 -R /tmp/tmp_${subject:4} && rm -rf /tmp/tmp_${subject:4}