RF: Only create wrappers if env vars look correct - $FSLDIR == $PREFIX, and

FSL_CREATE_WRAPPER_SCRIPTS is non-empty. Use

etc/fslconf/createFSLWrapper.sh

-#!/bin/sh
+#!/usr/bin/env bash
 #
 # Create wrapper scripts in $FSLDIR/share/fsl/bin/ which invoke commands that
 # are installed in $FSLDIR/bin/.
@@ -12,6 +12,13 @@
 # fslinstaller.py script - it is not intended to be used when individual
 # FSL projects are explicitly installed into a custom conda environment.
 #
+# Wrapper scripts will only be created if the following conditions are met:
+#  - The $FSLDIR and $PREFIX environment variables are set, and
+#    are equivalent
+#  - The $FSL_CREATE_WRAPPER_SCRIPTS environment variable is set and is not
+#    empty.
+#  -
+#
 # Early versions of this script would create symlinks from $FSLDIR/bin/ into
 # $FSLDIR/fslpython/envs/fslpython/bin/ (and, later, into
 # $FSLDIR/share/fsl/bin/). However, wrapper scripts are now used instead to
@@ -30,64 +37,71 @@
 #    to have a shebang line pointing to $FSLDIR/bin/python which does not
 #    exceed 127 characters.
 
+# Only create wrappers if the FSL_CREATE_WRAPPER_SCRIPTS
+# environment variable is set
+if [ -z "$FSL_CREATE_WRAPPER_SCRIPTS" ]; then
+  exit 0
+fi
+
+# Only create wrappers if FSLDIR exists
+if [ ! -d "$FSLDIR" ]; then
+  exit 0
+fi
+
+# and if FSLDIR == PREFIX
+if [ "$FSLDIR" != "$PREFIX" ]; then
+  exit 0
+fi
+
 # Names of all executables for which wrapper
 # scripts are to be created are passed as
 # arguments
 targets=$@
 
-# Only create wrappers if scripts
-# are in subdirectory of FSLDIR
-if [ -z "$FSLDIR" ]; then
-  exit 1
-fi
-
-case "$PREFIX" in "$FSLDIR"*)
-
-  for script in $targets; do
-    sourceScript="${PREFIX}/bin/$script"
-    targetScript="${FSLDIR}/share/fsl/bin/$script"
+for script in $targets; do
+  sourceScript="${PREFIX}/bin/$script"
+  targetScript="${FSLDIR}/share/fsl/bin/$script"
 
-    if [ ! -f "$sourceScript" ]; then
-      continue
-    fi
+  if [ ! -f "$sourceScript" ]; then
+    continue
+  fi
 
-    # create share/fsl/bin/ if it doesn't
-    # already exist
-    if [ ! -e "$FSLDIR/share/fsl/bin" ]; then
-      mkdir -p "$FSLDIR/share/fsl/bin"
-    fi
+  # create share/fsl/bin/ if it doesn't
+  # already exist
+  if [ ! -e "$FSLDIR/share/fsl/bin" ]; then
+    mkdir -p "$FSLDIR/share/fsl/bin"
+  fi
 
-    # remove target script if it already exists
-    if [ -e "$targetScript" ]; then
-      rm "$targetScript"
-    fi
+  # remove target script if it already exists
+  if [ -e "$targetScript" ]; then
+    rm "$targetScript"
+  fi
 
-    # Figure out whether this is a python
-    # executable or some other type of
-    # executable. We search for these strings
-    # in source file headers to ID them as
-    # python scripts. We need to check both
-    # match "#!/usr/bin/env python" and
-    # "#!<fsldir>/bin/python...", because
-    # conda might generate one or the other
-    # in different scenarios.
-    id1=$(head -c 1024 "$sourceScript" | grep "#!/usr/bin/env python")
-    id2=$(head -c 1024 "$sourceScript" | grep "/fslpython/bin/python")
+  # Figure out whether this is a python
+  # executable or some other type of
+  # executable. We search for these strings
+  # in source file headers to ID them as
+  # python scripts. We need to check both
+  # match "#!/usr/bin/env python" and
+  # "#!<fsldir>/bin/python...", because
+  # conda might generate one or the other
+  # in different scenarios.
+  id1=$(head -c 1024 "$sourceScript" | grep "#!/usr/bin/env python")
+  id2=$(head -c 1024 "$sourceScript" | grep "#!${FSLDIR%/}/bin/python")
 
-    # Non-python executable - use a
-    # pass-through script
-    if [ -z "$id1" ] && [ -z "$id2" ]; then
-      echo "#!/bin/sh"                   > "$targetScript"
-      echo "$FSLDIR/bin/$script \"$@\"" >> "$targetScript"
-    else
+  # Non-python executable - use a
+  # pass-through script
+  if [ -z "$id1" ] && [ -z "$id2" ]; then
+    echo "#!/usr/bin/env bash"         > "$targetScript"
+    echo "$FSLDIR/bin/$script "'"$@"' >> "$targetScript"
+  else
 
-      # Python executable - run it via
-      # $FSLDIR/bin/python in isolated mode
-      echo "#!/bin/sh"                                   > "$targetScript"
-      echo "$FSLDIR/bin/python -I $sourceScript \"$@\"" >> "$targetScript"
-    fi
+    # Python executable - run it via
+    # $FSLDIR/bin/python in isolated mode
+    echo "#!/usr/bin/env bash"                         > "$targetScript"
+    echo "$FSLDIR/bin/python -I $sourceScript "'"$@"' >> "$targetScript"
+  fi
 
-    # Preserve file permissions
-    chmod --reference="$sourceScript" "$targetScript"
-  done
-esac
+  # Preserve file permissions
+  chmod --reference="$sourceScript" "$targetScript"
+done

etc/fslconf/removeFSLWrapper.sh

-#!/bin/sh
+#!/usr/bin/env bash
 #
 # Remove wrapper script/links in $FSLDIR/share/fsl/bin/ which invoke commands
 # that are installed in $FSLDIR/bin/.  See createFSLWrapper.sh for more