From 03b5fbf8a452e6a4a0783c02519de0adb794e7b5 Mon Sep 17 00:00:00 2001
From: kliment-olechnovic <kliment.olechnovic@gmail.com>
Date: Sun, 13 Nov 2022 18:41:47 +0100
Subject: [PATCH] Added export LC_ALL=C in bash wrappers to avoid sort/join
 errors.

---
 expansion_js/voronota-js-fast-iface-cadscore  |  6 +++--
 .../voronota-js-fast-iface-cadscore-matrix    |  6 +++--
 .../voronota-js-fast-iface-data-graph         |  6 +++--
 expansion_js/voronota-js-fast-iface-voromqa   |  6 +++--
 expansion_js/voronota-js-iface-visualize      |  6 +++--
 expansion_js/voronota-js-ifeatures-voromqa    |  6 +++--
 expansion_js/voronota-js-ligand-cadscore      |  6 +++--
 expansion_js/voronota-js-membrane-voromqa     |  6 +++--
 expansion_js/voronota-js-only-global-voromqa  |  6 +++--
 expansion_js/voronota-js-voromqa              |  6 +++--
 voronota-cadscore                             | 23 +++++++++++--------
 voronota-contacts                             | 23 +++++++++++--------
 voronota-membrane                             |  6 +++--
 voronota-pocket                               |  6 +++--
 voronota-volumes                              | 23 +++++++++++--------
 voronota-voromqa                              | 23 +++++++++++--------
 16 files changed, 100 insertions(+), 64 deletions(-)

diff --git a/expansion_js/voronota-js-fast-iface-cadscore b/expansion_js/voronota-js-fast-iface-cadscore
index 15a3fab95..ecaca6983 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 b5128bc0e..d9922e54e 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 fd263a916..da37c76e7 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 173b1ed4f..d6d67dd57 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 fbc758763..64d880b49 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 7a549379d..81dbdb92e 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 63e0080ed..ad2b3cf31 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 17a24fcba..f502756c8 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 2fbc44abf..eab7a8d9f 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 a09c97d4c..af57f7869 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 8a85542a7..4262618e4 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 4df893d91..c408a1a74 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 cd734d0df..0dad768d2 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 3282df15a..9f280fee0 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 9d28f7c8b..9b68d4da9 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 395819ef6..bc3dc2247 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