scripts are automatically run locally if --sge option is not used

metaclade2

@@ -13,6 +13,12 @@
 #  with MetaCLADE2. If not, see <https://cecill.info/>.
 #
 
+# Pressing CTRL-C will stop the whole execution of the script
+trap ctrl_c INT; function ctrl_c() { exit 5; }
+# Exit from this script causes child processes (pending jobs) to stop execution
+trap 'kill $(jobs -p)' EXIT
+
+
 CMD_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd)
 CMD_NAME=$(basename "${BASH_SOURCE[0]}")
 SCRIPTS_DIR="${CMD_DIR}"/scripts
@@ -20,9 +26,6 @@ SCRIPTS_DIR="${CMD_DIR}"/scripts
 # Include common definitions
 source "${CMD_DIR}/metaclade2-common"
 
-# Pressing CTRL-C will stop the whole execution of the script
-trap ctrl_c INT; function ctrl_c() { exit 5; }
-
 # Definition of functions and global variables specific to this script
 
 MCLADE_LIB_PATH=""
@@ -235,47 +238,56 @@ print_status "MetaCLADE working directory: ${MCLADE_WORKDIR}"
 print_status "creating MetaCLADE script/job files"
 python3 "${SCRIPTS_DIR}/mclade_create_jobs.py" -i "${INPUT_FASTA}" -N "${MCLADE_JOBNAME}" ${MCLADE_DOMARG} -W "${MCLADE_WORKDIR}" -e "${MCLADE_EVALUECUTOFF}" -E "${MCLADE_EVALUECUTCONF}" -j "${NJOBS}" ${MCLADE_DAMAARG}
 
-# Possibly run MetaCLADE scripts in a SGE environment
-if [ "${MCLADE_USESGE}" = true ] ; then
-    # submit search jobs
-    print_status "submitting search jobs"
-    pidarr=()
-    for i in $(seq 1 ${NJOBS}); do
-        f="${MCLADE_WORKDIR}/jobs/1_search/${MCLADE_JOBNAME}_${i}.sh"
-        # run a qsub job for each non-empty script
-        if [ -f "${f}" ] && [ -s "${f}" ]; then
-            CMD="${PEXEC_CMD} ${f}"
-            qsub $SGE_QUEUEARG $SGE_TIMELIMARG -e ${MCLADE_WORKDIR}/log/search_${i}.err -o ${MCLADE_WORKDIR}/log/search_${i}.out -cwd -sync yes -N ${MCLADE_JOBNAME} -pe ${SGE_PENAME} ${NTHREADS} -b y "${CMD}" 2>&1 >"${MCLADE_WORKDIR}/log/search_qsub_${i}.log" &
+# Run MetaCLADE scripts (possibly using SGE)
+
+## SEARCH JOBS
+print_status "running search jobs"
+pidarr=()
+for i in $(seq 1 ${NJOBS}); do
+    f="${MCLADE_WORKDIR}/jobs/1_search/${MCLADE_JOBNAME}_${i}.sh"
+    # run a qsub job for each non-empty script
+    if [ -f "${f}" ] && [ -s "${f}" ]; then
+        CMD="${PEXEC_CMD} ${f}"
+        if [ "${MCLADE_USESGE}" = true ]; then
+            (qsub $SGE_QUEUEARG $SGE_TIMELIMARG -e ${MCLADE_WORKDIR}/log/search_${i}.err -o ${MCLADE_WORKDIR}/log/search_${i}.out -cwd -sync yes -N ${MCLADE_JOBNAME} -pe ${SGE_PENAME} ${NTHREADS} -b y "${CMD}" &>"${MCLADE_WORKDIR}/log/search_qsub_${i}.log") &
             pid=$!
             pidarr[$i]=$pid
+        else
+            ${CMD} >"${MCLADE_WORKDIR}/log/search_${i}.out" 2>"${MCLADE_WORKDIR}/log/search_${i}.err"
+            cmdret=$?; if (( cmdret != 0 )); then print_error "search job ${i} failed (exit status: ${cmdret})"; exit 1; fi
         fi
-    done
-    # wait search jobs to finish
-    print_status "waiting the search jobs to finish"
+    fi
+done
+# wait search jobs to finish
+if [ "${MCLADE_USESGE}" = true ]; then
+    print_status "waiting search jobs to finish"
     for i in ${!pidarr[@]}; do
         wait ${pidarr[${i}]}
-        pret=$?
-        if ((pret != 0)); then
-            echo "search job ${i} failed (exit status: ${pret})"
-            exit 1
-        fi
+        pret=$?; if ((pret != 0)); then print_error "search job ${i} failed (exit status: ${pret})"; exit 1; fi
     done
-    print_status "search jobs finished successfully"
+fi
+print_status "search jobs finished successfully"
 
-    # submit filter jobs
-    print_status "submitting filter ijobs"
-    unset pidarr; pidarr=()
-    for i in $(seq 1 ${NJOBS}); do
-        f="${MCLADE_WORKDIR}/jobs/2_filter/${MCLADE_JOBNAME}_${i}.sh"
-        # run a qsub job for each non-empty script
-        if [ -f "${f}" ] && [ -s "${f}" ]; then
-            CMD="${PEXEC_CMD} ${f}"
+## FILTER JOBS
+print_status "running filter jobs"
+unset pidarr; pidarr=()
+for i in $(seq 1 ${NJOBS}); do
+    f="${MCLADE_WORKDIR}/jobs/2_filter/${MCLADE_JOBNAME}_${i}.sh"
+    # run a qsub job for each non-empty script
+    if [ -f "${f}" ] && [ -s "${f}" ]; then
+        CMD="${PEXEC_CMD} ${f}"
+        if [ "${MCLADE_USESGE}" = true ]; then
             qsub $SGE_QUEUEARG $SGE_TIMELIMARG -e "${MCLADE_WORKDIR}/log/filter_${i}.err" -o "${MCLADE_WORKDIR}/log/filter_${i}.out" -cwd -sync yes -N ${MCLADE_JOBNAME} -pe ${SGE_PENAME} ${NTHREADS} -b y "${CMD}" 2>&1 >"${MCLADE_WORKDIR}/log/filter_qsub_${i}.log" &
             pid=$!
             pidarr[$i]=$pid
+        else
+            ${CMD} >"${MCLADE_WORKDIR}/log/filter_${i}.out" 2>"${MCLADE_WORKDIR}/log/filter_${i}.err"
+            cmdret=$?; if (( cmdret != 0 )); then print_error "filter job ${i} failed (exit status: ${cmdret})"; exit 1; fi
         fi
-    done
-    # wait search jobs to finish
+    fi
+done
+# wait search jobs to finish
+if [ "${MCLADE_USESGE}" = true ]; then
     print_status "waiting the filter jobs to finish"
     for i in ${!pidarr[@]}; do
         wait ${pidarr[${i}]}
@@ -285,16 +297,19 @@ if [ "${MCLADE_USESGE}" = true ] ; then
             exit 1
         fi
     done
-    print_status "search jobs finished successfully"
+fi
+print_status "search jobs finished successfully"
 
-    # create architecture
-    print_status "computing architecture"
-    f="${MCLADE_WORKDIR}/jobs/3_arch/${MCLADE_JOBNAME}.sh"
+## ARCHITECTURE JOBS
+print_status "running architecture job"
+f="${MCLADE_WORKDIR}/jobs/3_arch/${MCLADE_JOBNAME}.sh"
+if [ "${MCLADE_USESGE}" = true ]; then
     qsub $SGE_QUEUEARG $SGE_TIMELIMARG -e "${MCLADE_WORKDIR}/log/arch.err" -o "${MCLADE_WORKDIR}/log/arch.out" -cwd -sync yes -N ${MCLADE_JOBNAME} -pe ${SGE_PENAME} 1 -b y ${PEXEC_CMD} ${f} 2>&1 >>"${MCLADE_WORKDIR}/log/arch_qsub.log"
-    qret=$?
-    if ((qret != 0)); then
-        echo "architecture job failed (exit status: ${qret})"
-        exit 1
-    fi
-    print_status "architecture job finished successfully"
+    qret=$?; if ((qret != 0)); then print_error "architecture job failed (exit status: ${qret})"; exit 1; fi
+else
+    ${PEXEC_CMD} ${f} 2>"${MCLADE_WORKDIR}/log/arch.out" >"${MCLADE_WORKDIR}/log/arch.err"
+    cmdret=$?; if (( cmdret != 0 )); then print_error "architecture job failed (exit status: ${cmdret})"; exit 1; fi
 fi
+print_status "architecture job finished successfully"
+
+