ENH: New option in createFSLWrapper to generate wrapper script with different

name to executable

share/fsl/sbin/createFSLWrapper

 #!/usr/bin/env bash
 #
 # Create wrapper scripts in $FSLDIR/share/fsl/bin/ which invoke commands that
-# are installed in $FSLDIR/bin/.
+# are installed in $FSLDIR/bin/. Calling this script like:
 #
-# This script is used to create isolated versions of all executables provided
-# by FSL projects, so they can be added to the user $PATH without any other
-# executables that are installed into the FSL conda environment (for example,
-# python, pip, tcl, etc).
+#   createFSLWrapper command1 command2 command3
 #
-# This script is intended to be called by the post-link.sh script of the conda
-# recipe for each FSL project that provides executable commands.
+# will cause wrapper scripts to be created in $FSLDIR/share/fsl/bin/, which
+# call the commands of the same name in $FSLDIR/bin/, i.e.:
 #
-# This script should only be invoked when FSL is being installed via the
-# fslinstaller script - it is not intended to be used when individual FSL
-# projects are explicitly installed into a custom conda environment.
-#
-# The fslinstaller script should ensure that the FSLDIR and
-# FSL_CREATE_WRAPPER_SCRIPTS variables are set appropriately before creating
-# the FSL 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.
-#
-# Wrapper scripts, and not sym-links, are used to avoid a couple of potential
-# problems:
-#
-#  - We need python executables to exclusively use the libraries installed in
-#    the FSL conda environment. Users may have other Python environments
-#    activated, and/or libraries installed into a local site-packages
-#    directory. So we need to invoke the python interpreter in isolated mode,
-#    with the -I flag:
-#
-#        https://docs.python.org/3/using/cmdline.html#id2
-#
-#  - There is no guarantee that a shell supports shebang lines longer than 127
-#    characters. Depending on where FSL is installed, it may not be possible
-#    to have a shebang line pointing to $FSLDIR/bin/python which does not
-#    exceed 127 characters.
-#
-# Wrapper scripts are created for *all* FSL commands, including FSL TCL GUI
-# commands (e.g. "fsl", "Flirt", "Flirt_gui", etc).  FSL TCL GUIs are called
-# (e.g.) "<Command>" om Linux, but "<Command>_gui" on macOS, because macOS
-# file systems are usually case-sensitive.
-#
-# To work around this, and to not accidentally create a link called <Command>
-# to <command>, the FSL package post link scripts must only specify
-# "<Command>_gui", and *not* "<Command>".  This script will create a wrapper
-# script for the appropriate variant ("<Command>_gui" on macOS, or "<Command>"
-# on Linux).
+#    $FSLDIR/share/fsl/bin/command1 calls $FSLDIR/bin/command1
+#    $FSLDIR/share/fsl/bin/command2 calls $FSLDIR/bin/command2
 
 # Names of all executables for which wrapper
 # scripts are to be created are passed as
@@ -75,16 +33,27 @@ if [ "${FSLDIR}" != "${PREFIX}" ]; then
 fi
 
 
-for targetName in ${targets}; do
+for target in ${targets}; do
+
+  # A wrapper script with a different
+  # name to the target can be created
+  # by passing "targetName=wrapperName"
+  if [[ "${target}" == *"="* ]]; then
+    wrapper=${target#*=}
+    target=${target%=*}
+  else
+    wrapper=${target}
+  fi
 
-  target="${PREFIX}/bin/${targetName}"
+  target="${FSLDIR}/bin/${target}"
+  wrapper="${FSLDIR}/share/fsl/bin/${wrapper}"
 
   # Wrapper script for a FSL TCL GUI - here,
   # we remove the _gui suffix if the target
   # file does not exist (in which case we are
   # likely running on Linux).
-  if [[ "${targetName}" == *"_gui" ]] && [ ! -f "${target}" ]; then
-    targetName=${targetName/%_gui}
+  if [[ "${target}" == *"_gui" ]] && [ ! -f "${target}" ]; then
+    wrapper=${wrapper/%_gui}
     target=${target/%_gui}
   fi
 
@@ -97,8 +66,6 @@ for targetName in ${targets}; do
     continue
   fi
 
-  wrapper="${FSLDIR}/share/fsl/bin/${targetName}"
-
   # create share/fsl/bin/ if it doesn't
   # already exist
   if [ ! -e "${FSLDIR}/share/fsl/bin" ]; then

share/fsl/sbin/removeFSLWrapper

 #!/usr/bin/env bash
 #
 # Remove wrapper script/links in $FSLDIR/share/fsl/bin/ which invoke commands
-# that are installed in $FSLDIR/bin/.  See createFSLWrapper for more
+# that are installed in $FSLDIR/bin/. See createFSLWrapper for more
 # information.
 #
 # This script is intended to be called by the pre-unlink.sh script of the
@@ -19,25 +19,36 @@ targets="$@"
 # delete any wrapper scripts that exist.
 
 # Only remove wrappers if FSLDIR exists
-if [ ! -d "$FSLDIR" ]; then
+if [ ! -d "${FSLDIR}" ]; then
   exit 0
 fi
 
 # and if FSLDIR == PREFIX
-if [ "$FSLDIR" != "$PREFIX" ]; then
+if [ "${FSLDIR}" != "${PREFIX}" ]; then
   exit 0
 fi
 
 # Only remove if scripts are in subdirectory of FSLDIR
-for script in $targets; do
-  targetScript="${FSLDIR}/share/fsl/bin/$script"
+for target in ${targets}; do
+
+  # A wrapper script with a different
+  # name to the target can be created
+  # by passing "targetName=wrapperName"
+  if [[ "${target}" == *"="* ]]; then
+    wrapper=${target#*=}
+    target=${target%=*}
+  else
+    wrapper=${target}
+  fi
+
+  wrapper="${FSLDIR}/share/fsl/bin/${wrapper}"
 
   # See comment about FSL GUIs in post-link.sh
-  if [[ "$targetScript" == *"_gui" ]] && [ ! -f "$targetScript" ]; then
-    targetScript=${targetScript/_gui/}
+  if [[ "${target}" == *"_gui" ]] && [ ! -f "${wrapper}" ]; then
+    wrapper=${wrapper/%_gui}
   fi
 
-  if [ -f "$targetScript" ]; then
-    rm "$targetScript"
+  if [ -f "${wrapper}" ]; then
+    rm "${wrapper}"
   fi
 done