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FROM ubuntu:24.04
# Set args
ARG GITHUB_ACTIONS_USER_NAME="runner"
ARG GITHUB_ACTIONS_USER_ID="1001"
ARG GITHUB_ACTIONS_GROUP_NAME="docker"
ARG GITHUB_ACTIONS_GROUP_ID="121"
ARG CONDA_ENV_NAME="cwl-ica"
ARG YQ_VERSION="v4.35.2"
ARG ICAV2_CLI_VERSION="2.27.0"
ARG ICAV2_PLUGINS_CLI_VERSION="v2.27.0"
ARG ICAV2_PLUGINS_CLI_CONDA_PYTHON_VERSION="3.12"
ARG ICAV2_PLUGINS_CLI_CONDA_ENV_NAME="python3.12"
ARG CWL_UTILS_REPO_PATH="https://github.com/alexiswl/cwl-utils"
ARG CWL_UTILS_REPO_BRANCH="enhancement/cwl-inputs-schema-gen"
ARG MINIFORGE_NAME="Miniforge3"
ARG MINIFORGE_VERSION="24.3.0-0"
ARG TARGETPLATFORM="linux/amd64"
ENV CONDA_DIR=/opt/conda
RUN export DEBIAN_FRONTEND=noninteractive && \
( \
echo "Updating Apt" 1>&2 && \
apt update -y -q && \
echo "Installing jq, nodejs, rsync, graphviz and parallel" 1>&2 && \
apt install -y -q \
jq \
nodejs \
rsync \
graphviz \
parallel \
gcc \
python3-dev \
curl \
build-essential \
automake \
autoconf \
libtool \
unzip \
nghttp2 \
libnghttp2-dev \
libssl-dev \
wget \
autoconf \
busybox \
bzip2 \
ca-certificates \
git \
tini && \
echo "Cleaning up after apt installations" 1>&2 && \
apt clean -y -q \
) && \
( \
echo "Installing conda" 1>&2 && \
CONDA_TARGETPLATFORM_NAME="$(echo "${TARGETPLATFORM#linux/}" | sed 's/amd64/x86_64/g')" && \
echo "https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_NAME}-${MINIFORGE_VERSION}-Linux-${CONDA_TARGETPLATFORM_NAME}.sh" && \
wget --no-hsts --quiet \
--output-document /tmp/miniforge.sh \
"https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_NAME}-${MINIFORGE_VERSION}-Linux-${CONDA_TARGETPLATFORM_NAME}.sh" && \
/bin/bash /tmp/miniforge.sh -b -p ${CONDA_DIR} && \
rm /tmp/miniforge.sh && \
echo "Updating conda" 1>&2 && \
"${CONDA_DIR}/bin/conda" update --yes \
--name base \
--channel conda-forge \
--channel defaults \
conda && \
"${CONDA_DIR}/bin/conda" clean --tarballs --index-cache --packages --yes && \
find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \
find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \
"${CONDA_DIR}/bin/conda" clean --force-pkgs-dirs --all --yes && \
echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc && \
echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc \
) && \
( \
echo "Installing yq" 1>&2 && \
wget --quiet \
--output-document /usr/bin/yq \
"https://github.com/mikefarah/yq/releases/download/${YQ_VERSION}/yq_linux_amd64" && \
chmod +x /usr/bin/yq \
) && \
( \
echo "Installing gh binary" && \
curl --fail --silent --show-error --location \
"https://cli.github.com/packages/githubcli-archive-keyring.gpg" | \
dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | \
tee /etc/apt/sources.list.d/github-cli.list > /dev/null && \
apt update -y -q && \
apt install gh -y -q && \
apt clean -y -q \
) && \
( \
echo "Installing aws cli" 1>&2 && \
wget --quiet "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" \
--output-document "awscliv2.zip" && \
unzip -qq awscliv2.zip && \
./aws/install && \
rm -rf aws/ awscliv2.zip \
) && \
( \
echo "Installing ICAv2 CLI" 1>&2 && \
wget --quiet \
--output-document "/dev/stdout" \
"https://stratus-documentation-us-east-1-public.s3.amazonaws.com/cli/${ICAV2_CLI_VERSION}/ica-linux-${TARGETPLATFORM#linux/}.zip" | \
busybox unzip -p - "linux-${TARGETPLATFORM#linux/}/icav2" > "/usr/local/bin/icav2" && \
chmod +x "/usr/local/bin/icav2" \
) && \
( \
echo "Adding user groups" 1>&2 && \
addgroup \
--gid "${GITHUB_ACTIONS_GROUP_ID}" \
"${GITHUB_ACTIONS_GROUP_NAME}" && \
adduser \
--disabled-password \
--gid "${GITHUB_ACTIONS_GROUP_ID}" \
--uid "${GITHUB_ACTIONS_USER_ID}" \
"${GITHUB_ACTIONS_USER_NAME}" \
)
# Copy over source to . for user to install
COPY . "/cwl-ica-src-temp/"
RUN ( \
rsync \
--archive --remove-source-files \
--chown "${GITHUB_ACTIONS_USER_ID}:${GITHUB_ACTIONS_GROUP_ID}" "/cwl-ica-src-temp/" "/home/${GITHUB_ACTIONS_USER_NAME}/cwl-ica-src/" \
)
# Switch to conda user
USER "${GITHUB_ACTIONS_USER_NAME}"
ENV USER="${GITHUB_ACTIONS_USER_NAME}"
ENV PATH="${CONDA_DIR}/bin:${PATH}"
# Add conda command
RUN ( \
echo "Adding in package and env paths to conda arc" 1>&2 && \
conda config --append pkgs_dirs "\$HOME/.conda/pkgs" && \
conda config --append envs_dirs "\$HOME/.conda/envs" && \
echo "Installing into a conda env" 1>&2 && \
( \
cd "/home/${GITHUB_ACTIONS_USER_NAME}" && \
bash "cwl-ica-src/install.sh" -y -s && \
rm -rf "cwl-ica-src/" \
) \
)
# Set environment variables for user
ENV CONDA_PREFIX="/home/${GITHUB_ACTIONS_USER_NAME}/.conda/envs/${CONDA_ENV_NAME}"
ENV CONDA_DEFAULT_ENV="${CONDA_ENV_NAME}"
RUN ( \
cd "/home/${GITHUB_ACTIONS_USER_NAME}" && \
echo "Creating ${ICAV2_PLUGINS_CLI_CONDA_ENV_NAME} environment for icav2 cli plugins" 1>&2 && \
conda create --yes \
--name "${ICAV2_PLUGINS_CLI_CONDA_ENV_NAME}" \
python="${ICAV2_PLUGINS_CLI_CONDA_PYTHON_VERSION}" && \
echo "Installing ICAv2 CLI Plugins" 1>&2 && \
wget --quiet \
--output-document "icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}.zip" \
"https://github.com/umccr/icav2-cli-plugins/releases/download/${ICAV2_PLUGINS_CLI_VERSION}/icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}.zip" && \
unzip -qq "icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}.zip" && \
PATH="/home/${GITHUB_ACTIONS_USER_NAME}/.conda/envs/${ICAV2_PLUGINS_CLI_CONDA_ENV_NAME}/bin:${PATH}" \
bash "icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}/install.sh" "--no-autocompletion" && \
rm -rf "icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}" "icav2-plugins-cli--${ICAV2_PLUGINS_CLI_VERSION}.zip" \
)
# Add conda env to path
ENV PATH="/home/${GITHUB_ACTIONS_USER_NAME}/.conda/envs/${CONDA_ENV_NAME}/bin:${PATH}"
# Set ICAv2 CLI plugins home
ENV ICAV2_CLI_PLUGINS_HOME="/home/${GITHUB_ACTIONS_USER_NAME}/.icav2-cli-plugins/"
# Add cwl-utils (with cwl-inputs-schema-gen) to cwl-ica environment
RUN ( \
cd "/home/${GITHUB_ACTIONS_USER_NAME}" && \
echo "Cloning cwl-utils" 1>&2 && \
git clone --branch "${CWL_UTILS_REPO_BRANCH}" "${CWL_UTILS_REPO_PATH}" "cwl-utils" && \
echo "Installing cwl-utils" 1>&2 && \
( \
cd 'cwl-utils' && \
"/home/${GITHUB_ACTIONS_USER_NAME}/.conda/envs/${CONDA_ENV_NAME}/bin/pip" install . \
) && \
echo "Cleaning up" 1>&2 && \
rm -rf cwl-utils \
)
# Set entrypoint
CMD "cwl-ica"