add extra kernels

images/aomlomics-jh/Dockerfile

@@ -1,4 +1,3 @@
-# devcontainer-focused Rocker
 FROM docker.io/aomlomics/tourmaline:latest
 
 USER root
@@ -14,9 +13,18 @@ RUN echo "Creating ${NB_USER} user..." \
     # Make sure that /srv is owned by non-root user, so we can install things there
     && chown -R ${NB_USER}:${NB_USER} /srv
 
-# add the packages needed for jupyterhubs
+# add the packages needed for jupyterhubs to the base environment
 COPY jhub-environment.yml jhub-environment.yml
 RUN conda env update --name base -f jhub-environment.yml && conda clean --all
 
+# add packages needed for extra kernels in the notebooks
+RUN conda env update --name snakemake ipykernel && conda clean --all
+RUN conda env update --name qiime2-2023.5 ipykernel && conda clean --all
+
+# Register the kernels so you can open in notebooks
+RUN python -m ipykernel install --prefix /srv/conda/envs/snakemake --name snakemake --display-name snakemake
+RUN python -m ipykernel install --prefix /srv/conda/envs/qiime2-2023.5 --name qiime2-2023.5 --display-name qiime2
+USER ${NB_USER}
+
 USER ${NB_USER} 
 WORKDIR /home/${NB_USER}

images/aomlomics-jh/jhub-environment.yml

@@ -10,6 +10,7 @@ dependencies:
   - jupyterlab-git
   - jupyterlab-favorites
   - jupyter-resource-usage
+  - nb_conda_kernels
 #  - conda-lock
 ## VS code  
 #  - code-server >=3.2