# Use a specific ies base image
FROM registry-vpc.miracle.ac.cn/infcprelease/ies:v1.0.0
# Download the womtool JAR file from the Broad Institute repository
RUN wget -P /usr/local/lib https://github.com/broadinstitute/cromwell/releases/download/85/womtool-85.jar
# Update package list with a retry mechanism to ensure availability
RUN apt-get update || apt-get update
# Install essential packages: iputils-ping for network diagnostics, OpenJDK 21 for Java execution
# Clean up package cache to reduce image size
RUN apt-get install -y iputils-ping openjdk-21-jdk \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Install the pybioos Python package using conda's pip
RUN /opt/conda/bin/pip install pybioos
# Install the uv package, possibly for running a web server or API
RUN /opt/conda/bin/pip install uv mcp
# Install the Claude Dev VSCode extension for code-server in a specified directory
RUN mkdir -p /opt/code-server/extensions && \
/app/code-server/bin/code-server --extensions-dir /opt/code-server/extensions --install-extension saoudrizwan.claude-dev
# Clone the bioos-mcp-server repository into the specified directory
RUN git clone https://github.com/GBA-BI/bioos-mcp-server.git /opt/lib/bioos-mcp-server
# Copy and set appropriate permissions for the script that initializes code-server
COPY --chmod=755 ./images/ies/etc/s6-overlay/s6-rc.d/init-code-server/run /etc/s6-overlay/s6-rc.d/init-code-server/run
COPY --chmod=755 ./bin/womtool /bin/womtool
# Create configuration directory and write settings for the VSCode extension
RUN mkdir -p /home/ies/.local/share/code-server/User/globalStorage/saoudrizwan.claude-dev/settings && \
cat <<EOF > /home/ies/.local/share/code-server/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
{
"mcpServers": {
"bioos": {
"command": "uv",
"args": [
"--directory",
"/opt/lib/bioos-mcp-server/src/bioos_mcp",
"run",
"/opt/lib/bioos-mcp-server/src/bioos_mcp/bioos_mcp_server.py"
],
"env": {
"PYTHONPATH": "/opt/lib/bioos-mcp-server/src"
}
}
}
}
EOF
