studyforrest-ppa-analysis/code/generate_2nd-lvl-design_audio-ppa-grp.sh

#!/bin/bash

set -e
set -u

cat << EOT > code/compute_2nd-lvl_audio-ppa-grp.submit
# auto-generate file (generate_2nd_level_design.sh) -- do not modify!
universe = vanilla
output = condor_logs/\$(CLUSTER).\$(PROCESS).out
error = condor_logs/\$(CLUSTER).\$(PROCESS).err
log = condor_logs/\$(CLUSTER).\$(PROCESS).log
getenv = True
request_cpus = 1
request_memory = 5000
should_transfer_files = NO
transfer_executable = False
initialdir = /data/project/studyforrest_ppa
executable = \$ENV(FSLDIR)/bin/feat

EOT

label="2nd-lvl_audio-ppa-grp"

for sub in sub-*; do
  subid=$(echo "$sub" | cut -d '-' -f2-)
  sed -e "s/###SUB###/sub-${subid}/g" code/2nd-lvl_audio-ppa-grp.fsf > "$sub/${label}.fsf"
  printf "arguments = $sub/${label}.fsf\nqueue\n" >> code/compute_2nd-lvl_audio-ppa-grp.submit
done