add correct handling of apptainer

run_transparent_singularity.sh

@@ -215,19 +215,27 @@ singularity exec $singularity_opts --pwd $_base $container $_base/ts_binaryFinde
 echo "create singularity executable for each regular executable in commands.txt"
 # $@ parses command line options.
 #test   executable="fslmaths"
-singularity_version=$(singularity version | cut -d'-' -f1)
+
+# The --env option requires singularity > 3.6 or apptainer. Test here:
 required_version="3.6"
+if which apptainer >/dev/null 2>&1; then
+    echo "Apptainer is installed."
+    singularity_version=3.6
+else
+    echo "Apptainer is not installed. Testing for singularity version."
+    singularity_version=$(singularity version | cut -d'-' -f1)
+fi
+
 while read executable; do \
    echo $executable > $_base/${executable}; \
    echo "#!/usr/bin/env bash" > $executable
    echo "export PWD=\`pwd -P\`" >> $executable
+
    # neurodesk_singularity_opts is a global variable that can be set in neurodesk for example --nv for gpu support
    # --silent is required to suppress bind mound warnings (e.g. for /etc/localtime)
    # --cleanenv is required to prevent environment variables on the host to affect the containers (e.g. Julia and R packages), but to work 
    # correctly with GUIs, the DISPLAY variable needs to be set as well. This only works in singularity >= 3.6.0
-
    if printf '%s\n' "$required_version" "$singularity_version" | sort -V | head -n1 | grep -q "$required_version"; then
-      echo "Singularity version is equal to or newer than $required_version. All features should work."
       echo "singularity --silent exec --cleanenv --env DISPLAY=\$DISPLAY \$neurodesk_singularity_opts --pwd \$PWD $_base/$container $executable \"\$@\"" >> $executable
    else
       echo "Singularity version is older than $required_version. GUIs will not work correctly!"