From 4bada7494af609ca9bf37c1ea6a48c41e27f62cb Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Sun, 25 Feb 2018 21:38:02 +0100
Subject: [PATCH] MNT Use a different variable for FATAL type and command
---
bin/submitjob | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/bin/submitjob b/bin/submitjob
index a407b15..b0e248a 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
--
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