CORR_cat12.8.1/code/process.sub

#!/bin/bash

subject=$(basename $1)
subd="$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#     a configured URL is outdated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#6c5791d8-1803-48a1-bbaa-2b5e23b5f707 \
  /data/project/cat_preprocessed/dataladstore/6c5/791d8-1803-48a1-bbaa-2b5e23b5f707 \
  ${subd} \
  "

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

${executable} ${arguments} \
> /data/project/cat_preprocessed/TMP/CAT12.8/CORR_cat12.8.1/logs/${subject}.out \
2> /data/project/cat_preprocessed/TMP/CAT12.8/CORR_cat12.8.1/logs/${subject}.err

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