Adding Docker Image to run Viash on Saturn Cloud

docker/Dockerfile

@@ -0,0 +1,84 @@
+from dataintuitive/viash:latest
+
+RUN rm -rf /etc/apt/sources.list.d/sbt*
+RUN mkdir /opt/conda && \
+    ln -s /opt/conda /srv/conda
+ENV APP_BASE=/srv
+ENV CONDA_DIR=/srv/conda
+ENV CONDA_BIN=${CONDA_DIR}/bin
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get -qq update && \
+    apt-get -qq upgrade -y && \
+    apt-get -qq install --yes --no-install-recommends \
+        gettext-base \
+        gnupg \
+        locales \
+        wget \
+        curl \
+        bzip2 \
+        ca-certificates \
+        ssh \
+        file \
+        git \
+        awscli \
+        rsync \
+        sudo \
+        openssh-server \
+        htop \
+        screen \
+     > /dev/null && \
+    apt-get -qq purge && \
+    apt-get -qq clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    mkdir -p /run/sshd && \
+    chmod 755 /run/sshd && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+ENV SHELL /bin/bash
+ENV NB_USER=jovyan
+ENV NB_UID=1000
+ENV USER=${NB_USER}
+ENV HOME=/home/${NB_USER}
+
+RUN adduser --disabled-password \
+    --gecos "Default user" \
+    --uid ${NB_UID} \
+    ${NB_USER} && \
+    echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook && \
+    mkdir -p ${APP_BASE} && \
+    chown 1000:1000 -R /opt/conda && \
+    chown -R $NB_USER:$NB_USER ${APP_BASE}
+USER ${NB_USER}
+
+COPY install-miniconda.bash /tmp/install-miniconda.bash
+RUN bash /tmp/install-miniconda.bash
+COPY install-jupyter.bash /tmp/install-jupyter.bash
+COPY environment.yml /tmp/environment.yml
+RUN  bash /tmp/install-jupyter.bash && \
+    echo '' > ${CONDA_DIR}/conda-meta/history && \
+    ${CONDA_BIN}/conda config --system --add channels conda-forge && \
+    ${CONDA_BIN}/conda config --system --set auto_update_conda false && \
+    ${CONDA_BIN}/conda config --system --set show_channel_urls true
+ENV NPM_DIR ${APP_BASE}/npm
+ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/saturn
+ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_BIN}:${NPM_DIR}/bin:${HOME}/.local/bin:${PATH}
+WORKDIR ${HOME}
+
+USER root
+RUN curl -s https://get.nextflow.io | bash && \
+    mv nextflow /usr/local/bin
+
+
+COPY requirements.txt /tmp/requirements.txt
+RUN /opt/conda/bin/conda install -n saturn python=3.7 pip ipykernel
+RUN /opt/conda/envs/saturn/bin/pip install --no-cache-dir -r /tmp/requirements.txt
+# install AWS CLI
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+RUN unzip -q awscliv2.zip
+RUN ./aws/install
+RUN /opt/conda/envs/saturn/bin/python -m ipykernel install --name python3 --display-name 'saturn (Python 3)' --prefix=/opt/conda
+
+USER ${NB_USER}

docker/environment.yml

@@ -0,0 +1,23 @@
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - nodejs
+  - python
+  - ipywidgets
+  - jupyterlab-git
+  - jupyterlab=2.2.9
+  - nbconvert
+  - notebook
+  - jupyter-server-proxy
+  - dask-core
+  - distributed
+  - dask-labextension
+  - yarl
+  - pyviz_comms
+  - jupyterlab_code_formatter=1.3.8
+  - black
+  - isort
+  - tornado
+  - nbdime
+  - voila

docker/install-jupyter.bash

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -ex
+export PATH="${CONDA_BIN}:${PATH}"
+
+cd $(dirname $0)
+
+echo "installing root env:"
+cat /tmp/environment.yml
+conda install -c conda-forge mamba
+mamba env update -n root  -f /tmp/environment.yml
+jupyter serverextension enable --sys-prefix jupyter_server_proxy
+jupyter serverextension enable dask_labextension --sys-prefix
+jupyter serverextension enable --py jupyterlab_code_formatter --sys-prefix
+
+# jupyter labextension install @bokeh/jupyter_bokeh
+# jupyter labextension install @jupyter-widgets/jupyterlab-manager
+# jupyter labextension install dask-labextension@3.0.0
+# jupyter labextension install @ryantam626/jupyterlab_code_formatter
+# jupyter labextension install @pyviz/jupyterlab_pyviz
+# jupyter labextension install jupyterlab-execute-time
+# jupyter labextension install @telamonian/theme-darcula
+# jupyter labextension install jupyterlab-python-file
+
+conda clean -afy
+jupyter lab clean
+jlpm cache clean
+npm cache clean --force
+find ${CONDA_DIR}/ -type f,l -name '*.pyc' -delete
+find ${CONDA_DIR}/ -type f,l -name '*.a' -delete
+find ${CONDA_DIR}/ -type f,l -name '*.js.map' -delete
+rm -rf $HOME/.node-gyp
+rm -rf $HOME/.local
+
+conda create -n saturn

docker/install-miniconda.bash

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+set -ex
+
+cd $(dirname $0)
+
+MINICONDA_VERSION=py37_4.9.2
+URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/miniconda-installer.sh
+wget --quiet $URL -O ${INSTALLER_PATH}
+chmod +x ${INSTALLER_PATH}
+
+MD5SUM="3143b1116f2d466d9325c206b7de88f7"
+
+if ! echo "${MD5SUM}  ${INSTALLER_PATH}" | md5sum  --quiet -c -; then
+    echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"
+    exit 1
+fi
+
+bash ${INSTALLER_PATH} -b -p ${CONDA_DIR} -f
+
+export PATH="${CONDA_BIN}:$PATH"
+
+# Update conda
+conda update -y conda
+
+# Allow easy direct installs from conda forge
+conda config --system --add channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true

docker/profile

@@ -0,0 +1,23 @@
+if [ "${PS1-}" ]; then
+  if [ "${BASH-}" ] && [ "$BASH" != "/bin/sh" ]; then
+    # The file bash.bashrc already sets the default PS1.
+    # PS1='\h:\w\$ '
+    if [ -f /etc/bash.bashrc ]; then
+      . /etc/bash.bashrc
+    fi
+  else
+    if [ "`id -u`" -eq 0 ]; then
+      PS1='# '
+    else
+      PS1='$ '
+    fi
+  fi
+fi
+if [ -d /etc/profile.d ]; then
+  for i in /etc/profile.d/*.sh; do
+    if [ -r $i ]; then
+      . $i
+    fi
+  done
+  unset i
+fi

docker/requirements.txt

@@ -0,0 +1 @@
+numpy