input SGE parameters are now handled

metaclade2

@@ -35,7 +35,7 @@ NTHREADS=1
 NJOBS=16
 
 function print_usage() {
-    echo -en "\n  USAGE: ${CMD_NAME} -i <input_fasta> [options]\n"
+    echo -en "\n  USAGE: ${CMD_NAME} -i <input_fasta> -N <name> [options]\n"
     echo -en "\n"
     echo -en "  MANDATORY OPTIONS:\n
     -i, --input <path>\tInput file of AA sequences in FASTA format\n
@@ -56,18 +56,26 @@ function print_usage() {
     " | column -t -s $'\t'
 	echo -en "\n"
 	echo -en "  OTHER OPTIONS:\n
-    --SGE\tRun MetaCLADE jobs on a SGE HPC environment\n
-    -t, --threads <num>\tNumber of threads for each job (default:${NTHREADS})\n
     -j, --jobs <num>\tNumber of jobs to be created (default:${NJOBS})\n
+    -t, --threads <num>\tNumber of threads for each job (default:${NTHREADS})\n
     -h, --help\tPrint this help message\n
     -V, --version\tPrint version\n" | column -t -s $'\t'
     echo -en "\n"
+    echo -en "  SGE OPTIONS:\n
+    --sge\tRun MetaCLADE jobs on a SGE HPC environment\n
+    --pe <name>\tParallel environment to use (mandatory)\n
+    --queue <name>\tName of a specific queue where jobs are submitted\n
+    --time-limit <hh:mm:ss>\tTime limit for submitted jobs formatted as hh:mm:ss\n
+                           \twhere hh, mm, ss represent hours, minutes, and seconds respectively\n
+                           \t(e.g., use --time-limit 2:30:00 for setting a limit of 2h and 30m)\n
+    " | column -t -s $'\t'
+    echo -en "\n"
 }
 
 
 # retrieve provided arguments
 opts="i:N:ad:D:e:E:W:t:j:hV"
-longopts="input:,name:,arch,domain-list:,domain-file:,evalue-cutoff:,evalue-cutconf:,work-dir,SGE,threads:,jobs:,help,version"
+longopts="input:,name:,arch,domain-list:,domain-file:,evalue-cutoff:,evalue-cutconf:,work-dir,threads:,jobs:,help,version,sge,pe:,queue:,time-limit:"
 ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
 if [ $? -ne 0 ] || [ $# -eq 0 ]; then # do not change the order of this test!
     print_usage
@@ -108,9 +116,6 @@ while [ -n "${1}" ]; do
             shift
             MCLADE_WORKDIR=${1}
             ;;
-        --SGE)
-            MCLADE_USESGE=true
-            ;;
         -t|--threads)
             shift
             NTHREADS=${1}
@@ -127,6 +132,21 @@ while [ -n "${1}" ]; do
             print_version
             exit 0
             ;;
+        --sge)
+            MCLADE_USESGE=true
+            ;;
+        --pe)
+            shift
+            SGE_PENAME=${1}
+            ;;
+        --queue)
+            shift
+            SGE_QUEUE=${1}
+            ;;
+        --time-limit)
+            shift
+            SGE_TIMELIM=${1}
+            ;;
         --)
             shift
             break
@@ -185,7 +205,7 @@ check_cmds "python3"
 # Validate SGE parameters
 if [ "${MCLADE_USESGE}" = true ] ; then
     if [ -z ${SGE_PENAME} ]; then
-        print_error "you must set a parallel environment name with -P|--parallel-env option along with the --SGE option"
+        print_error "you must set a parallel environment name with -P|--pe option along with the --sge option"
         exit 1
     fi
     if [ ! -z ${SGE_QUEUE} ]; then
@@ -238,8 +258,7 @@ if [ "${MCLADE_USESGE}" = true ] ; then
 
     # submit filter jobs
     print_status "submitting filter ijobs"
-    unset pidarr
-    pidarr=()
+    unset pidarr; pidarr=()
     for i in $(seq 1 ${NJOBS}); do
         f="${MCLADE_WORKDIR}/jobs/1_filter/${MCLADE_JOBNAME}_${i}.sh"
         # run a qsub job for each non-empty script