diff --git a/docker/Dockerfile b/docker/Dockerfile index 6917a7e..a7081d4 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -97,6 +97,10 @@ RUN . ${FSLDIR}/etc/fslconf/fsl.sh && \ nilearn \ mne +RUN . ${FSLDIR}/etc/fslconf/fsl.sh && \ + git clone https://github.com/MIC-DKFZ/HD-BET && \ + cd HD-BET && \ + pip install -e . # Clone MRtrix3 repository WORKDIR /opt @@ -111,7 +115,7 @@ RUN ./configure -nogui && \ ENV PATH="/opt/mrtrix3/bin:${PATH}" -RUN wget -nv "https://filesender.reannz.co.nz/download.php?token=624deb75-7c1e-4c96-ad9f-826e65e89630&files_ids=24775" \ +RUN wget -nv https://github.com/nesi/training-environment-jupyter-matai-app/releases/download/v0.1.0/data.zip \ -O /var/lib/data.zip \ && unzip /var/lib/data.zip -d /var/lib \ && rm -f /var/lib/data.zip \ @@ -120,7 +124,6 @@ RUN wget -nv "https://filesender.reannz.co.nz/download.php?token=624deb75-7c1e-4 -# Verify installations: This is more of a sanity check as there were previous tags didn't -# have these two packages correctly installed yet the container build didn't fail +# Verify installations RUN python3 -c "import nilearn; import mne" || exit 1 diff --git a/submit.yml.erb b/submit.yml.erb index 6946342..7ff84fa 100644 --- a/submit.yml.erb +++ b/submit.yml.erb @@ -17,7 +17,7 @@ script: native: container: name: "matai" - image: "ghcr.io/nesi/training-environment-jupyter-matai-app:v1.0.0" + image: "ghcr.io/nesi/training-environment-jupyter-matai-app:v1.1.0" command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"] working_dir: "<%= Etc.getpwnam(ENV['USER']).dir %>" restart_policy: 'OnFailure'