Add Allen Institute OpenScope image

.github/workflows/docker-push.yaml

@@ -17,6 +17,8 @@ jobs:
         include:
           - tag: latest
             dockerfile: Dockerfile
+          - tag: latest
+            dockerfile: Dockerfile.openscope
           - tag: latest-allensdk
             dockerfile: Dockerfile.allensdk
           - tag: latest-gpu
@@ -51,4 +53,4 @@ jobs:
           tags: |
             ${{ secrets.DOCKERHUB_DANDIHUB_USERNAME }}/dandihub:${{ matrix.tag }}
           cache-from: type=registry,ref=${{ secrets.DOCKERHUB_DANDIHUB_USERNAME }}/dandihub:${{ matrix.tag }}
-          cache-to: type=inline
+          cache-to: type=inline

.github/workflows/docker-test.yaml

@@ -15,6 +15,8 @@ jobs:
         include:
           - tag: latest
             dockerfile: Dockerfile
+          - tag: latest
+            dockerfile: Dockerfile.openscope
           - tag: latest-allensdk
             dockerfile: Dockerfile.allensdk
           - tag: latest-gpu
@@ -41,4 +43,4 @@ jobs:
           file: ./images/${{ matrix.dockerfile }}
           push: false
           cache-from: type=registry,ref=${{ secrets.DOCKERHUB_DANDIHUB_USERNAME }}/dandihub:${{ matrix.tag }}
-          cache-to: type=inline
+          cache-to: type=inline

Makefile

@@ -0,0 +1,6 @@
+.PHONY: dev
+OCI_ENGINE?= podman
+dev-image:
+	@echo "Building development image from $(CONTAINERFILE)..."
+	$(OCI_ENGINE) build -f $(CONTAINERFILE) -t dev-image:latest .
+	$(OCI_ENGINE) run --rm -p 8888:8888 --name dev_jupyterlab dev-image:latest start-notebook.sh --NotebookApp.token=""

README.md

@@ -26,6 +26,7 @@ This Terraform blueprint creates a Kubernetes environment (EKS) and installs Jup
 - [Adjusting Core Node](#adjusting-core-node)
 - [Upgrading Kubernetes](#upgrading-kubernetes)
 - [Kubernetes Layer Tour](#kubernetes-layer-tour)
+- [Additional Image options](#creating-images)
 
 ## Prerequisites
 
@@ -447,3 +448,11 @@ Finally, remove the ec2 instance.
 ```sh
 ./.github/scripts/cleanup-ec2.sh
 ```
+
+## Creating Additional Images
+
+The following command will build and run a new image, which can be viewed locally in the browser at 127.0.0.1:8888/
+
+```sh
+make dev-image CONTAINERFILE=images/Dockerfile.openscope
+```

envs/shared/jupyterhub.yaml

@@ -56,6 +56,11 @@ singleuser:
               default: true
               kubespawner_override:
                 image: "${singleuser_image_repo}:${singleuser_image_tag}-allensdk"
+            openscope:
+              display_name: "OpenScope"
+              default: true
+              kubespawner_override:
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-openscope"
       kubespawner_override:
         image_pull_policy: Always
         cpu_limit: 2
@@ -109,6 +114,11 @@ singleuser:
               default: true
               kubespawner_override:
                 image: "${singleuser_image_repo}:${singleuser_image_tag}-allensdk"
+            openscope:
+              display_name: "OpenScope"
+              default: true
+              kubespawner_override:
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-openscope"
             matlab:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:
@@ -143,6 +153,11 @@ singleuser:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:
                 image: "${singleuser_image_repo}:${singleuser_image_tag}-matlab"
+            openscope:
+              display_name: "OpenScope"
+              default: true
+              kubespawner_override:
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-openscope"
       kubespawner_override:
         image_pull_policy: Always
         cpu_limit: 24
@@ -167,6 +182,11 @@ singleuser:
               default: true
               kubespawner_override:
                 image: "${singleuser_image_repo}:${singleuser_image_tag}-allensdk"
+            openscope:
+              display_name: "OpenScope"
+              default: true
+              kubespawner_override:
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-openscope"
             matlab:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:
@@ -195,6 +215,11 @@ singleuser:
               default: true
               kubespawner_override:
                 image: "${singleuser_image_repo}:${singleuser_image_tag}-gpu-allensdk"
+            openscope:
+              display_name: "OpenScope"
+              default: true
+              kubespawner_override:
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-openscope"
             matlab:
               display_name: "MATLAB GPU (must provide your own license)"
               kubespawner_override:

images/Dockerfile.openscope

@@ -0,0 +1,75 @@
+FROM quay.io/jupyter/datascience-notebook:python-3.11.10
+
+USER root
+
+RUN apt update \
+ && apt install -y software-properties-common \
+ && add-apt-repository -y 'ppa:apptainer/ppa' \
+ && apt update \
+ && apt install -y apptainer-suid \
+ && rm -rf /var/lib/apt/lists/* && rm -rf /tmp/*
+
+RUN apt-get update && apt-get install -y ca-certificates libseccomp2 \
+   s3fs netbase less parallel tmux screen vim emacs htop curl \
+   && rm -rf /var/lib/apt/lists/* && rm -rf /tmp/*
+
+RUN curl --silent --show-error "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" \
+  -o "awscliv2.zip" && unzip awscliv2.zip \
+  && ./aws/install && rm -rf ./aws awscliv2.zip
+
+# Install jupyter server proxy and desktop
+RUN curl -fsSLo /usr/share/keyrings/brave-browser-archive-keyring.gpg https://brave-browser-apt-release.s3.brave.com/brave-browser-archive-keyring.gpg \
+   && echo "deb [signed-by=/usr/share/keyrings/brave-browser-archive-keyring.gpg] https://brave-browser-apt-release.s3.brave.com/ stable main"|sudo tee /etc/apt/sources.list.d/brave-browser-release.list \
+   && apt-get -y -qq update \
+   && apt-get -y -qq install \
+        dbus-x11 \
+        xfce4 \
+        xfce4-panel \
+        xfce4-session \
+        xfce4-settings \
+        xorg \
+        xubuntu-icon-theme \
+        brave-browser \
+        tigervnc-standalone-server \
+        tigervnc-xorg-extension \
+    # chown $HOME to workaround that the xorg installation creates a
+    # /home/jovyan/.cache directory owned by root
+   && chown -R $NB_UID:$NB_GID $HOME \
+   && rm -rf /var/lib/apt/lists/* && rm -rf /tmp/*
+
+# apt-get may result in root-owned directories/files under $HOME
+RUN mkdir /opt/extras && chown -R $NB_UID:$NB_GID $HOME /opt/extras
+
+USER $NB_USER
+
+RUN pip install --no-cache-dir jupyter-remote-desktop-proxy
+
+ENV MAMBA_NO_LOW_SPEED_LIMIT=1
+
+RUN mamba install --yes 'datalad>=0.18' rclone 'h5py>3.3=mpi*' ipykernel zarr blosc eccodes websockify \
+  && wget --quiet https://raw.githubusercontent.com/DanielDent/git-annex-remote-rclone/v0.8/git-annex-remote-rclone \
+  && chmod +x git-annex-remote-rclone && mv git-annex-remote-rclone /opt/conda/bin \
+  && conda clean --all -f -y && rm -rf /tmp/*
+
+RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \
+    datalad-osf dandi nibabel nilearn pybids spikeinterface neo itkwidgets \
+    'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]"  \
+    aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
+    webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
+    tensorstore anndata
+
+RUN pip install --no-cache-dir multiscale_spatial_image jupyterlab-git \
+        datalad-fuse
+
+RUN pip install --no-cache-dir brainrender napari
+
+# Leaving "standard" Dockerfile copy above as-is to simplify later switch to modular builds.
+USER root
+
+RUN apt-get install -y coreutils libgl1 libglx-mesa0 libglib2.0-0 && rm -rf /var/lib/apt/lists/* /tmp/*
+
+USER $NB_USER
+
+RUN cd /tmp \
+  && git clone https://github.com/AllenInstitute/openscope_databook.git \
+  && pip install --no-cache-dir -e './openscope_databook[dev]'