Merge pull request #198 from NeuroDesk:bug_fix_environment_variables_…

…in_notebooks

set environment variable SINGULARITY_BINDPATH

Dockerfile

@@ -385,6 +385,9 @@ RUN cp -rp /home/${NB_USER} /tmp/
 # Set up data directory so it exists in the container for the SINGULARITY_BINDPATH
 RUN mkdir -p /data
 
+
+
+
 # Install neurocommand
 ADD "https://api.github.com/repos/neurodesk/neurocommand/git/refs/heads/main" /tmp/skipcache
 RUN rm /tmp/skipcache \
@@ -403,4 +406,6 @@ ADD "https://api.github.com/repos/neurodesk/example-notebooks/git/refs/heads/mai
 RUN rm /home/${NB_USER}/skipcache \
     && git clone --depth 1 https://github.com/NeuroDesk/example-notebooks
 
+# Set SINGULARITY_BINDPATH and MODULEPATH here so it's available within a notebook (the startup scripts set these things too late):
+ENV SINGULARITY_BINDPATH=/data,/neurodesktop-storage,/tmp,/cvmfs,/home/${NB_USER}:/home/matlab/.matlab/R2022a_licenses,/home/${NB_USER}:/opt/matlab/R2022a/licenses
 ENV MODULEPATH=/cvmfs/neurodesk.ardc.edu.au/containers/modules/

config/jupyter/environment_variables.sh

@@ -27,7 +27,9 @@ if [ -d /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules ]; then
         export MODULEPATH=`echo $MODULEPATH | sed 's/ /:/g'`
 fi
 
+# This also needs to be set in the Dockerfile, so it is available in a jupyter notebook
 export SINGULARITY_BINDPATH=/data,/neurodesktop-storage,/tmp,/cvmfs,/home/${NB_USER}:/home/matlab/.matlab/R2022a_licenses,/home/${NB_USER}:/opt/matlab/R2022a/licenses
+# This also needs to be set in the Dockerfile, so it is available in a jupyter notebook
 
 export SINGULARITYENV_SUBJECTS_DIR=/home/${NB_USER}/freesurfer-subjects-dir
 export MPLCONFIGDIR=/home/${NB_USER}/.config/matplotlib-mpldir