Merge commit 'e9e2e72ff034fa42d44037a7e762ba97e18af541'

neurodesk/transparent-singularity/run_transparent_singularity.sh

@@ -243,11 +243,18 @@ while read executable; do \
    # --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
+   # --bind is needed to handle non-default temp directories (Github issue #11)
+   for customtmp in TMP TMPDIR TEMP TEMPDIR; do
+      eval tmpvar=\$$customtmp
+      if [[ -n $tmpvar ]]; then
+         bindtmpdir="--bind \$$customtmp:/tmp"
+      fi
+   done
    if printf '%s\n' "$required_version" "$singularity_version" | sort -V | head -n1 | grep -q "$required_version"; then
-      echo "singularity --silent exec --cleanenv --env DISPLAY=\$DISPLAY \$neurodesk_singularity_opts --pwd \"\$PWD\" $_base/$container $executable \"\$@\"" >> $executable
+      echo "singularity --silent exec --cleanenv --env DISPLAY=\$DISPLAY $bindtmpdir \$neurodesk_singularity_opts --pwd \"\$PWD\" $_base/$container $executable \"\$@\"" >> $executable
    else
       echo "Singularity version is older than $required_version. GUIs will not work correctly!"
-      echo "singularity --silent exec --cleanenv \$neurodesk_singularity_opts --pwd \"\$PWD\" $_base/$container $executable \"\$@\"" >> $executable
+      echo "singularity --silent exec --cleanenv $bindtmpdir \$neurodesk_singularity_opts --pwd \"\$PWD\" $_base/$container $executable \"\$@\"" >> $executable
    fi
 
    chmod a+x $executable