operating system is now correctly checked

profileview-build

@@ -62,7 +62,7 @@ function print_usage() {
 # retrieve provided arguments
 opts="i:D:d:n:ft:j:hV"
 longopts="input:,domain-id:,db:,lib-name:,force,threads:,max-jobs:,help,version,cov:,qid:,max-id:,evalue:,iter:"
-if [ check_system = "Linux" ]; then
+if [ $(check_system) = "Linux" ]; then
     ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
     retcode=$?
 else

profileview-motif

@@ -58,7 +58,7 @@ function print_usage() {
 
 opts="l:m:o:W:t:hV"
 longopts="lib:,models:,out-dir:,temp-dir:,threads:,help,version"
-if [ check_system = "Linux" ]; then
+if [ $(check_system) = "Linux" ]; then
     ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
     retcode=$?
 else
@@ -145,7 +145,7 @@ fi
 
 # Create temp working directory
 if [ -z "${PV_TMPDIR}" ]; then
-    if [ check_system = "Linux" ]; then
+    if [ $(check_system) = "Linux" ]; then
         PV_TMPDIR=$(mktemp -p "${PWD}" -d pvtmp-XXXXX) || { print_error "cannot create temporary directory"; exit 1; }
     else
         PV_TMPDIR=$(mktemp -d "${PWD}"/pvtmp-XXXXX) || { print_error "cannot create temporary directory"; exit 1; }

profileview-tree

@@ -45,7 +45,7 @@ function print_usage() {
     echo -en "\n"
     echo -en "  OTHER OPTIONS:\n
     -k, --k-best <num>\tNumber of best-match models to retain for each sequence (default: ${PV_KBEST})\n
-    --cvar <num>\tMinimum explained variance threshold for selecting principal components before the clustering (default: ${PV_CVAR})
+    -c, --cvar <num>\tMinimum explained variance threshold for selecting principal components before the clustering (default: ${PV_CVAR})
                 \tThe provided value must be a number in the interval [0,1]\n
     -s, --seq-desc <name>\tInput sequence descriptor file, that is a CSV file containing the follwing fileds:\n
                          \t<sequence_id>,<function_id>,<family_id>,<sequence_length>\n
@@ -60,9 +60,9 @@ function print_usage() {
 
 # retrieve provided arguments
 
-opts="i:l:k:s:p:W:t:hV"
+opts="i:l:k:c:s:p:W:t:hV"
 longopts="input:,lib:,k-best:,seq-desc:,prefix:,temp-dir:,threads:,cvar:,help,version"
-if [ check_system = "Linux" ]; then
+if [ $(check_system) = "Linux" ]; then
     ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
     retcode=$?
 else
@@ -106,7 +106,7 @@ while [ -n "${1}" ]; do
             shift
             PV_KBEST=${1}
             ;;
-        --cvar)
+        -c|--cvar)
             shift
             PV_CVAR=${1}
             ;;
@@ -181,7 +181,7 @@ fi
 
 # Create temp working directory
 if [ -z "${PV_TMPDIR}" ]; then
-    if [ check_system = "Linux" ]; then
+    if [ $(check_system) = "Linux" ]; then
         PV_TMPDIR=$(mktemp -p "${PWD}" -d pvtmp-XXXXX) || { print_error "cannot create temporary directory"; exit 1; }
     else
         PV_TMPDIR=$(mktemp -d "${PWD}"/pvtmp-XXXXX) || { print_error "cannot create temporary directory"; exit 1; }