diff --git a/expansion_js/voronota-js-fast-iface-cadscore b/expansion_js/voronota-js-fast-iface-cadscore index 15a3fab9..ecaca698 100755 --- a/expansion_js/voronota-js-fast-iface-cadscore +++ b/expansion_js/voronota-js-fast-iface-cadscore @@ -56,11 +56,13 @@ fi if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } TARGET_INFILE="" diff --git a/expansion_js/voronota-js-fast-iface-cadscore-matrix b/expansion_js/voronota-js-fast-iface-cadscore-matrix index b5128bc0..d9922e54 100755 --- a/expansion_js/voronota-js-fast-iface-cadscore-matrix +++ b/expansion_js/voronota-js-fast-iface-cadscore-matrix @@ -45,11 +45,13 @@ ALLARGS=("$@") if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } RESTRICT_INPUT="[]" diff --git a/expansion_js/voronota-js-fast-iface-data-graph b/expansion_js/voronota-js-fast-iface-data-graph index fd263a91..da37c76e 100755 --- a/expansion_js/voronota-js-fast-iface-data-graph +++ b/expansion_js/voronota-js-fast-iface-data-graph @@ -80,11 +80,13 @@ fi if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/expansion_js/voronota-js-fast-iface-voromqa b/expansion_js/voronota-js-fast-iface-voromqa index 173b1ed4..d6d67dd5 100755 --- a/expansion_js/voronota-js-fast-iface-voromqa +++ b/expansion_js/voronota-js-fast-iface-voromqa @@ -83,11 +83,13 @@ fi if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/expansion_js/voronota-js-iface-visualize b/expansion_js/voronota-js-iface-visualize index fbc75876..64d880b4 100755 --- a/expansion_js/voronota-js-iface-visualize +++ b/expansion_js/voronota-js-iface-visualize @@ -31,11 +31,13 @@ ALLARGS=("$@") if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } diff --git a/expansion_js/voronota-js-ifeatures-voromqa b/expansion_js/voronota-js-ifeatures-voromqa index 7a549379..81dbdb92 100755 --- a/expansion_js/voronota-js-ifeatures-voromqa +++ b/expansion_js/voronota-js-ifeatures-voromqa @@ -41,11 +41,13 @@ ALLARGS=("$@") if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/expansion_js/voronota-js-ligand-cadscore b/expansion_js/voronota-js-ligand-cadscore index 63e0080e..ad2b3cf3 100755 --- a/expansion_js/voronota-js-ligand-cadscore +++ b/expansion_js/voronota-js-ligand-cadscore @@ -53,11 +53,13 @@ fi if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } TARGET_RECEPTOR="" diff --git a/expansion_js/voronota-js-membrane-voromqa b/expansion_js/voronota-js-membrane-voromqa index 17a24fcb..f502756c 100755 --- a/expansion_js/voronota-js-membrane-voromqa +++ b/expansion_js/voronota-js-membrane-voromqa @@ -45,11 +45,13 @@ ALLARGS=("$@") if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/expansion_js/voronota-js-only-global-voromqa b/expansion_js/voronota-js-only-global-voromqa index 2fbc44ab..eab7a8d9 100755 --- a/expansion_js/voronota-js-only-global-voromqa +++ b/expansion_js/voronota-js-only-global-voromqa @@ -52,11 +52,13 @@ fi if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/expansion_js/voronota-js-voromqa b/expansion_js/voronota-js-voromqa index a09c97d4..af57f786 100755 --- a/expansion_js/voronota-js-voromqa +++ b/expansion_js/voronota-js-voromqa @@ -72,11 +72,13 @@ ALLARGS=("$@") if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; } INFILE="" diff --git a/voronota-cadscore b/voronota-cadscore index 8a85542a..4262618e 100755 --- a/voronota-cadscore +++ b/voronota-cadscore @@ -42,6 +42,19 @@ exit 1 } readonly ZEROARG=$0 + +if [[ $ZEROARG == *"/"* ]] +then + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" + cd - &> /dev/null +fi + +export LC_ALL=C + +command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } +command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } + INFILE_TARGET_PDB="" INFILE_MODEL_PDB="" INPUT_FILTER_QUERY_PARAMETERS="" @@ -170,16 +183,6 @@ then print_help_and_exit fi -if [[ $ZEROARG == *"/"* ]] -then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH - cd - &> /dev/null -fi - -command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } -command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } - MD5SUM_COMMAND="md5sum" if command -v md5sum &> /dev/null then diff --git a/voronota-contacts b/voronota-contacts index 4df893d9..c408a1a7 100755 --- a/voronota-contacts +++ b/voronota-contacts @@ -32,6 +32,19 @@ exit 1 } readonly ZEROARG=$0 + +if [[ $ZEROARG == *"/"* ]] +then + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" + cd - &> /dev/null +fi + +export LC_ALL=C + +command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } +command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } + INFILE="" INPUT_FILTER_QUERY_PARAMETERS="" CONTACTS_QUERY_FIRST_PARAMETERS="--match-min-seq-sep 1" @@ -110,16 +123,6 @@ then print_help_and_exit fi -if [[ $ZEROARG == *"/"* ]] -then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH - cd - &> /dev/null -fi - -command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } -command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } - if $USE_HBPLUS then command -v hbplus &> /dev/null || { echo >&2 "Warning: 'hbplus' executable not in binaries path, thus no 'hb' tags will be assigned"; USE_HBPLUS=false; } diff --git a/voronota-membrane b/voronota-membrane index cd734d0d..0dad768d 100755 --- a/voronota-membrane +++ b/voronota-membrane @@ -28,11 +28,13 @@ readonly ZEROARG=$0 if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } command -v jq &> /dev/null || { echo >&2 "Error: 'jq' executable not in binaries path"; exit 1; } diff --git a/voronota-pocket b/voronota-pocket index 3282df15..9f280fee 100755 --- a/voronota-pocket +++ b/voronota-pocket @@ -51,11 +51,13 @@ readonly ZEROARG=$0 if [[ $ZEROARG == *"/"* ]] then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" cd - &> /dev/null fi +export LC_ALL=C + command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } command -v jq &> /dev/null || { echo >&2 "Error: 'jq' executable not in binaries path"; exit 1; } diff --git a/voronota-volumes b/voronota-volumes index 9d28f7c8..9b68d4da 100755 --- a/voronota-volumes +++ b/voronota-volumes @@ -27,6 +27,19 @@ exit 1 } readonly ZEROARG=$0 + +if [[ $ZEROARG == *"/"* ]] +then + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" + cd - &> /dev/null +fi + +export LC_ALL=C + +command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } +command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } + INFILE="" INPUT_FILTER_QUERY_PARAMETERS="" ATOMS_QUERY_PARAMETERS="" @@ -82,16 +95,6 @@ then print_help_and_exit fi -if [[ $ZEROARG == *"/"* ]] -then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH - cd - &> /dev/null -fi - -command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } -command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } - MD5SUM_COMMAND="md5sum" if command -v md5sum &> /dev/null then diff --git a/voronota-voromqa b/voronota-voromqa index 395819ef..bc3dc224 100755 --- a/voronota-voromqa +++ b/voronota-voromqa @@ -136,6 +136,19 @@ function substitute_ids_in_filename readonly ZEROARG=$0 ALLARGS=("$@") + +if [[ $ZEROARG == *"/"* ]] +then + cd "$(dirname ${ZEROARG})" + export PATH="$(pwd):${PATH}" + cd - &> /dev/null +fi + +export LC_ALL=C + +command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } +command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } + INFILE="" REFERENCE_SEQUENCE="" INPUT_FILTER_QUERY_PARAMETERS="" @@ -648,16 +661,6 @@ then PRINT_GLOBAL_SCORES_HEADER=true fi -if [[ "$ZEROARG" == *"/"* ]] -then - cd $(dirname $ZEROARG) - export PATH=$(pwd):$PATH - cd - &> /dev/null -fi - -command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; } -command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; } - MD5SUM_COMMAND="md5sum" if command -v md5sum &> /dev/null then