processing-workflow-tutorial/code/process.condor_submit

universe       = vanilla
# resource requirements for each job
request_cpus   = 1
request_memory = 4G
request_disk   = 5G

# tell condor that a job is self contained and the executable
# is enough to bootstrap the computation on the execute node
should_transfer_files = yes
# explicitly do not transfer anything back
# we are using datalad for everything that matters
transfer_output_files = ""

# the actual job script, nothing condor-specific in it
executable     = $ENV(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#     a configured URL is outdated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
environment = "\
  JOBID=$(subject).$(Cluster) \
  DSLOCKFILE=$ENV(PWD)/.condor_datalad_lock \
  DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__101cat='ria+http://containers.ds.inm7.de#{id}' \
  GIT_AUTHOR_NAME='Adina Wagner' \
  GIT_AUTHOR_EMAIL='adina.wagner@t-online.de' \
  "

# place the job logs into PWD/logs, using the same name as for the result branches
# (JOBID)
log    = $ENV(PWD)/logs/$(subject)_$(Cluster).log
output = $ENV(PWD)/logs/$(subject)_$(Cluster).out
error  = $ENV(PWD)/logs/$(subject)_$(Cluster).err
# essential args for 'participant_job'
# 1: where to clone the analysis dataset
# 2: location to push the result git branch to. The 'ria+' prefix is stripped.
# 3: ID of the subject to process
arguments = "\
  ria+file:///data/group/psyinf/inputstore#47a9ef9e-9fa0-49cd-873f-c51cc501da96 \
  /data/group/psyinf/outputstore/47a/9ef9e-9fa0-49cd-873f-c51cc501da96 \
  sub-$(subject) \
  "
queue