Update package_mrtrix for MRtrix3Tissue user experience

Similar to set_path, build and configure in earlier commits. Contemplated renaming this script accordingly, but decided to keep the name to avoid confusion. From the output folder name itself, as well as the command line feedback during the execution of the script, it should be obvious what the different context is.

Author: thijsdhollander

package_mrtrix

@@ -1,8 +1,8 @@
 #!/bin/bash
 cat <<EOF
 This script collates all the executables and runtime dependencies needed for
-MRtrix3, and creates a GZ compressed archive suitable for deployment on other
-systems. It takes all executables found in the bin/ folder and the MRtrix3
+MRtrix3Tissue, and creates a GZ compressed archive suitable for deployment on
+other systems. It takes all executables found in the bin/ folder and the mrtrix3
 library from the lib/ folder. It is up to the user to ./configure and ./build
 the software first.
 
@@ -26,24 +26,24 @@ echo -n "Press enter to proceed (or Ctrl-C to abort)..."
 read
 
 (
-  echo - collating MRtrix3 executables and library...
+  echo - collating MRtrix3Tissue executables and mrtrix3 library...
   set -e
-  mkdir -p _package/mrtrix3/
-  cp -r bin/ _package/mrtrix3/
-  cp -r lib/ _package/mrtrix3/ 
-  cp -r share/ _package/mrtrix3/ 
+  mkdir -p _package/MRtrix3Tissue/
+  cp -r bin/ _package/MRtrix3Tissue/
+  cp -r lib/ _package/MRtrix3Tissue/ 
+  cp -r share/ _package/MRtrix3Tissue/ 
 
   [ ${1:-"x"} == "-standalone" ] && (
-    cat > _package/mrtrix3/launcher <<"EOF"
+    cat > _package/MRtrix3Tissue/launcher <<"EOF"
 #!/bin/bash
 PREFIX="$(dirname $0)/.."
 COMMAND="$(basename $0)"
 "$PREFIX"/lib/ld-*.so* "$PREFIX"/exe/"$COMMAND" "$@"
 EOF
-    chmod a+x _package/mrtrix3/launcher
-    mkdir -p _package/mrtrix3/exe
+    chmod a+x _package/MRtrix3Tissue/launcher
+    mkdir -p _package/MRtrix3Tissue/exe
     (
-      cd _package/mrtrix3/bin
+      cd _package/MRtrix3Tissue/bin
       for n in *; do
       file $n | grep -q script || ( 
         mv $n ../exe
@@ -58,7 +58,7 @@ EOF
     for n in $LIBS; do
       if [ -e $n ]; then
         echo '        '$n;
-        cp $n _package/mrtrix3/lib/
+        cp $n _package/MRtrix3Tissue/lib/
       fi
     done
 
@@ -72,9 +72,9 @@ EOF
       echo '    additional libraries required for Qt:'
       for n in $QTLIBS; do echo '        '$n; done
 
-      cp $QTLIBS _package/mrtrix3/lib/
-      cp -r $QTPLUGDIR _package/mrtrix3/lib/
-      cat > _package/mrtrix3/lib/qt.conf << EOF
+      cp $QTLIBS _package/MRtrix3Tissue/lib/
+      cp -r $QTPLUGDIR _package/MRtrix3Tissue/lib/
+      cat > _package/MRtrix3Tissue/lib/qt.conf << EOF
 [Paths]
 Prefix = .
 EOF
@@ -86,16 +86,16 @@ EOF
 
 ) && cat <<EOF
 
-You can now copy the folder _package/mrtrix3 over to your target systems.
+You can now copy the folder _package/MRtrix3Tissue over to your target systems.
 For example packing it up using:
 
 $ cd _package
-$ tar cfz mrtrix3.tar.gz mrtrix3
+$ tar cfz MRtrix3Tissue.tar.gz MRtrix3Tissue
 
-On your target system, unpack mrtrix3.tar.gz using:
+On your target system, unpack MRtrix3Tissue.tar.gz using:
 
-$ tar xfz mrtrix3.tar.gz
+$ tar xfz MRtrix3Tissue.tar.gz
 
-You should also add the mrtrix3/bin to your PATH to finalise the installation.
+You should also add the MRtrix3Tissue/bin to your PATH to finalise the installation.
 EOF