diff --git a/bin/submitjob b/bin/submitjob index a407b15cb06d577e17449f62114aeae85ad986c1..b0e248a47402ef6c372b78e73ae5f4f7261a4bf2 100755 --- a/bin/submitjob +++ b/bin/submitjob @@ -106,7 +106,7 @@ usage() { echo >&2 " parallelizable pipelines such ngless and jug" echo >&2 "" echo >&2 " In addition to standard SGE/LSF/SLURM environment variables, the following" - echo >&2 " can be used in the jobs file referencing the values used." + echo >&2 " can be used in the jobs file to refer to the values specified/used." echo >&2 " \${Q_NAME} \${Q_CORES} \${Q_MEM} \${Q_MEMALL} \${Q_TIME} \${Q_ACTIVE}" echo >&2 " \${Q_QUEUE} \${Q_LOGFILE} \${Q_WAITFOR}" echo >&2 "" @@ -226,7 +226,7 @@ export Q_WAITFOR="${WAITFOR}" ${PRE_CMDS} # If requested, enable tracebacks only after pre-commands to avoid bash-strictness failures -${FATAL} +${FATAL_CMD} # Comments and empty lines are removed from the job submission script SELECTED_JOB=\$(echo '${JOBS_TO_RUN} @@ -275,7 +275,7 @@ export Q_WAITFOR="${WAITFOR}" ${PRE_CMDS} # If requested, enable tracebacks only after pre-commands to avoid bash-strictness failures -${FATAL} +${FATAL_CMD} # Comments and empty lines are removed from the job submission script SELECTED_JOB=\$(echo '${JOBS_TO_RUN} @@ -320,7 +320,7 @@ export Q_WAITFOR="${WAITFOR}" ${PRE_CMDS} # If requested, enable tracebacks only after pre-commands to avoid bash-strictness failures -${FATAL} +${FATAL_CMD} # Comments and empty lines are removed from the job submission script SELECTED_JOB=\$(echo '${JOBS_TO_RUN} @@ -475,7 +475,7 @@ JOBFILE="$1" if [ "$FATAL" == "fatal" ]; then _TRACEBACK="${_SELF_LOCATION}/../modules/helpers/traceback.bash" [ ! -f "$_TRACEBACK" ] && generic_error "Couldn't find helper module at '$_TRACEBACK'" - FATAL=". ${_TRACEBACK}" + FATAL_CMD=". ${_TRACEBACK}" fi prepare_jobs # defines PRE_CMDS and JOBS_TO_RUN