Use cluster-agnostic environment variables in runRscript

runRscript.sh was written for use with SGE, using SGE-specific
environment variables. Modify the script to process either SGE or
Slurm environment variables by setting cluster-agnostic variables
at the beginning of the script based on the SGE variables or the
Slurm variables, depending on are set. Then use these cluster-agnostic
variables in the remainder of the script.

Note: it would probably be better to have the Cluster subclasses
in TopmedPipeline.py set the proper variables for the script, if
we refactored the classes following #55.

runRscript.sh

@@ -1,15 +1,30 @@
 #! /bin/bash
 
+# TODO: UPDATE FOR SLURM?
+# Set cross-cluster environment variables.
+
+
+# Determine cluster type and set cluster-agnostic variables appropriate.
+if [[ ! -z "${SGE_ROOT}" ]]
+then
+  CLUSTER_JOB_ID=$JOB_ID
+  CLUSTER_TASK_ID=$SGE_TASK_ID
+elif [[ ! -z "${SLURM_CLUSTER_NAME}" ]]
+then
+  export CLUSTER_JOB_ID=$SLURM_JOB_ID
+  export CLUSTER_TASK_ID=$SLURM_ARRAY_TASK_ID
+fi
+
 # set MKL_NUM_THREADS to match number of available cores
-export MKL_NUM_THREADS=$NSLOTS
+export MKL_NUM_THREADS=$CLUSTER_SLOTS
 
 while getopts ":cs" opt; do
   case $opt in
     c)
-      TASK="--chromosome $SGE_TASK_ID"
+      TASK="--chromosome $CLUSTER_TASK_ID"
       ;;
     s)
-      TASK="--segment $SGE_TASK_ID"
+      TASK="--segment $CLUSTER_TASK_ID"
       ;;
     \?)
       echo "Invalid option: -$OPTARG" >&2
@@ -18,25 +33,25 @@ while getopts ":cs" opt; do
 done
 shift "$((OPTIND-1))"
 
-if [ "$SGE_TASK_ID" == "undefined" ] || [ "$SGE_TASK_ID" == "" ]; then
+if [ "$CLUSTER_TASK_ID" == "undefined" ] || [ "$CLUSTER_TASK_ID" == "" ]; then
     TASK=""
 fi
 
 args=("$@") # all arguments
 unset args[0] # remove first argument (R script name)
 tb=`date`
-echo ">>> Start job: $JOB_ID at $tb ... "
+echo ">>> Start job: $CLUSTER_JOB_ID at $tb ... "
 R -q --vanilla --args ${args[@]} $TASK < $1
 
 
 R_exit_code="$?"
 r_status=$R_exit_code
 if [[ $R_exit_code -ne "0" ]]; then
   echo ">>> Error: R status code $R_exit_code"
-  if [[ "$SGE_TASK_ID" -ne "" ]]; then
-    touch fail.${JOB_ID}.${SGE_TASK_ID}
+  if [[ "$CLUSTER_TASK_ID" -ne "" ]]; then
+    touch fail.${CLUSTER_JOB_ID}.${CLUSTER_TASK_ID}
   else
-    touch fail.${JOB_ID}
+    touch fail.${CLUSTER_JOB_ID}
   fi
   if [[ ! -z "${SGE_ROOT+x}" && ! -z "${ENABLE_EQW+x}" ]]; then
     r_status=100
@@ -45,5 +60,5 @@ if [[ $R_exit_code -ne "0" ]]; then
 fi
 
 te=`date`
-echo ">>> End job: $JOB_ID at $te"
+echo ">>> End job: $CLUSTER_JOB_ID at $te"
 exit $r_status