first working implementation of MetaCLADE with SGE support

metaclade2

@@ -243,19 +243,19 @@ if [ "${MCLADE_USESGE}" = true ] ; then
         f="${MCLADE_WORKDIR}/jobs/1_search/${MCLADE_JOBNAME}_${i}.sh"
         # run a qsub job for each non-empty script
         if [ -f "${f}" ] && [ -s "${f}" ]; then
-            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 ${PEXEC_CMD} ${f} &
+            CMD="${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" &
             pid=$!
             pidarr[$i]=$pid
-            ((i++))
         fi
     done
     # wait search jobs to finish
     print_status "waiting the search jobs to finish"
-    for i in ${!pidtab[@]}; do
-        wait ${pidtab[${i}]}
-        ret=$?
-        if ((ret != 0)); then
-            echo "MetaCLADE search job ${i} failed (exit status: ${ret})"
+    for i in ${!pidarr[@]}; do
+        wait ${pidarr[${i}]}
+        pret=$?
+        if ((pret != 0)); then
+            echo "search job ${i} failed (exit status: ${pret})"
             exit 1
         fi
     done
@@ -268,19 +268,19 @@ if [ "${MCLADE_USESGE}" = true ] ; then
         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
-            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 ${PEXEC_CMD} ${f} &
+            CMD="${PEXEC_CMD} ${f}"
+            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
-            ((i++))
         fi
     done
     # wait search jobs to finish
     print_status "waiting the filter jobs to finish"
-    for i in ${!pidtab[@]}; do
-        wait ${pidtab[${i}]}
-        ret=$?
-        if ((ret != 0)); then
-            echo "MetaCLADE filter job ${i} failed (exit status: ${ret})"
+    for i in ${!pidarr[@]}; do
+        wait ${pidarr[${i}]}
+        pret=$?
+        if ((pret != 0)); then
+            echo "filter job ${i} failed (exit status: ${pret})"
             exit 1
         fi
     done
@@ -289,10 +289,10 @@ if [ "${MCLADE_USESGE}" = true ] ; then
     # create architecture
     print_status "computing architecture"
     f="${MCLADE_WORKDIR}/jobs/3_arch/${MCLADE_JOBNAME}.sh"
-    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}
+    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=$?
     if ((qret != 0)); then
-        echo "error during MetaCLADE architecture step ($qret)"
+        echo "architecture job failed (exit status: ${qret})"
         exit 1
     fi
     print_status "architecture job finished successfully"