metaclade2 now accepts a custom config file to override some default settings

metaclade2

@@ -33,6 +33,7 @@ DAMA_OLPMAXDOM=50
 MCLADE_USEDAMA=false
 MCLADE_USESGE=false
 MCLADE_WORKDIR=${PWD}
+MCLADE_USERCFG_ARG=""
 MCLADE_OUTFILE=""
 MCLADE_RMTMP=false
 NTHREADS=4
@@ -57,6 +58,7 @@ function print_usage() {
     -D, --domain-file <path>\tFile that contains the Pfam accession numbers\n
                             \tof the domains to be considered (one per line)\n
     -W, --work-dir <path>\tWorking directory (default:current directory)\n
+    -U, --user-cfg <path>\tUser config file for overriding default MetaCLADE2 configuration\n
     --remove-temp\tRemove temporary intermediate files, keeping only results and logs\n
     " | column -t -s $'\t'
     echo -en "\n"
@@ -90,8 +92,8 @@ function print_usage() {
 
 
 # retrieve provided arguments
-opts="N:i:o:ad:D:e:E:W:t:j:hV"
-longopts="name:,input:,output:,arch,domain-list:,domain-file:,evalue-cutoff:,evalue-cutconf:,overlappingAA:,overlappingMaxDomain:,work-dir,remove-temp,threads:,jobs:,help,version,sge,pe:,queue:,time-limit:"
+opts="N:i:o:ad:D:e:E:W:U:t:j:hV"
+longopts="name:,input:,output:,arch,domain-list:,domain-file:,evalue-cutoff:,evalue-cutconf:,overlappingAA:,overlappingMaxDomain:,work-dir:,user-cfg:,remove-temp,threads:,jobs:,help,version,sge,pe:,queue:,time-limit:"
 ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
 if [ $? -ne 0 ] || [ $# -eq 0 ]; then # do not change the order of this test!
     print_usage
@@ -144,6 +146,10 @@ while [ -n "${1}" ]; do
             shift
             MCLADE_WORKDIR=${1}
             ;;
+        -U|--user-cfg)
+            shift
+            MCLADE_USERCFG_ARG="--config ${1}"
+            ;;
         --remove-temp)
             MCLADE_RMTMP=true
             ;;
@@ -272,7 +278,13 @@ print_status "creating MetaCLADE script/job files"
 python3 "${SCRIPTS_DIR}/mclade_create_jobs.py" \
     -i "${INPUT_FASTA}" -N "${MCLADE_JOBNAME}" ${MCLADE_DOMARG} -W "${MCLADE_WORKDIR}" \
     -e "${MCLADE_EVALUECUTOFF}" -E "${MCLADE_EVALUECUTCONF}" --overlappingAA ${DAMA_OLPAA} --overlappingMaxDomain ${DAMA_OLPMAXDOM} ${MCLADE_DAMAARG} \
-    -j "${NJOBS}" >"${MCLADE_WORKDIR}/log/mclade_create_jobs.out" 2>"${MCLADE_WORKDIR}/log/mclade_create_jobs.err"
+    -j "${NJOBS}" \
+    ${MCLADE_USERCFG_ARG} \
+    >"${MCLADE_WORKDIR}/log/mclade_create_jobs.out" 2>"${MCLADE_WORKDIR}/log/mclade_create_jobs.err"
+if [ $? -ne 0 ]; then
+    print_error "cannot create MetaCLADE job files"
+    exit 1
+fi
 
 # Run MetaCLADE scripts (possibly using SGE)
 
@@ -290,7 +302,7 @@ for i in $(seq 1 ${NJOBS}); do
             pidarr[$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 failed (exit status: ${cmdret})"; exit 1; fi
+            cmdret=$?; if [ $cmdret -ne 0 ]; then print_error "search job failed (exit status: ${cmdret})"; exit 1; fi
         fi
     fi
 done