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added devcontainer to brick-template
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FROM mcr.microsoft.com/devcontainers/python:3.9 | ||
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# Install necessary packages | ||
RUN apt-get update && apt-get install -y \ | ||
wget \ | ||
unzip \ | ||
xvfb \ | ||
libxi6 \ | ||
libgconf-2-4 \ | ||
libnss3-dev \ | ||
libxss1 \ | ||
libappindicator1 \ | ||
fonts-liberation \ | ||
libatk-bridge2.0-0 \ | ||
libgtk-3-0 \ | ||
libgbm1 \ | ||
libasound2 \ | ||
libdpkg-perl \ | ||
libatomic1 \ | ||
ca-certificates \ | ||
curl \ | ||
gnupg \ | ||
python3-venv \ | ||
awscli | ||
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# Install pipx and biobricks | ||
RUN python3 -m pip install --user pipx \ | ||
&& python3 -m pipx ensurepath | ||
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# Create /mnt/biobricks directory and set permissions | ||
RUN mkdir -p /mnt/biobricks/biobricks-ai \ | ||
&& chown -R vscode:vscode /mnt/biobricks | ||
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# Add pipx binaries to the PATH for all users | ||
RUN echo 'export PATH="$PATH:$HOME/.local/bin"' >> /etc/bash.bashrc \ | ||
&& echo 'export PATH="$PATH:$HOME/.local/bin"' >> /home/vscode/.bashrc | ||
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# Switch to vscode user to perform user-specific installations | ||
USER vscode | ||
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# Install Python dependencies | ||
COPY .devcontainer/requirements.txt /tmp/requirements.txt | ||
RUN pip install -r /tmp/requirements.txt | ||
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# Accept build argument for BIOBRICKS_TOKEN | ||
ARG BIOBRICKS_TOKEN | ||
ENV BIOBRICKS_TOKEN=${BIOBRICKS_PUBLIC_TOKEN} | ||
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# Install biobricks and configure it | ||
RUN /bin/bash -c 'source /etc/bash.bashrc && pipx install biobricks && biobricks version' \ | ||
&& /bin/bash -c 'if [ -z "$BIOBRICKS_TOKEN" ] || [ ${#BIOBRICKS_TOKEN} -lt 5 ]; then echo "BIOBRICKS_TOKEN is not set or is too short (less than 5 characters)"; exit 1; fi' \ | ||
&& /bin/bash -c 'source /etc/bash.bashrc && biobricks configure --bblib=/mnt/biobricks --token=${BIOBRICKS_TOKEN} --interactive=False' | ||
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# Switch back to root user to complete setup | ||
USER root |
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{ | ||
"name": "SMRT Development Container", | ||
"build": { | ||
"dockerfile": "Dockerfile", | ||
"context": "..", | ||
"args": { | ||
"BIOBRICKS_TOKEN": "${localEnv:BIOBRICKS_TOKEN}" | ||
} | ||
}, | ||
"features": { | ||
"ghcr.io/devcontainers/features/docker-in-docker:1": {} | ||
}, | ||
"customizations": { | ||
"vscode": { | ||
"settings": { | ||
"terminal.integrated.defaultProfile.linux": "bash", | ||
"python.pythonPath": "/usr/local/bin/python" | ||
}, | ||
"extensions": [ | ||
"ms-python.python", | ||
"ms-toolsai.jupyter", | ||
"ms-vsliveshare.vsliveshare", // Live Share extension | ||
"github.copilot", // GitHub Copilot extension | ||
"insilica.vscode-pycmd" | ||
] | ||
} | ||
}, | ||
"remoteUser": "vscode" | ||
} |
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python-dotenv==1.0.1 | ||
pandas==2.2.2 | ||
biobricks==0.3.7 | ||
fastparquet==2024.5.0 | ||
pyarrow==16.1.0 | ||
dvc==3.51.1 | ||
dvc-s3==3.2.0 |