066233b03c
Implemented SYSTEM_PACKAGES environment variable for flexible system library installation: Key Features: - Users specify packages in .env: SYSTEM_PACKAGES="libopenslide0 libgdal-dev" - Packages installed during Docker build (secure, no runtime mounting) - Automatic rebuild detection when packages change - Documentation with common scientific computing packages Technical Implementation: - ARG SYSTEM_PACKAGES in Dockerfile with conditional apt-get install - Build argument passed from claude-docker.sh script - Clean package management with cache cleanup Benefits: - Secure: No system directory mounting required - Flexible: Users choose exactly what they need - Documented: Common packages listed in README - Clean: Packages baked into image, not mounted at runtime Tested successfully with OpenSlide: conda run -n prism python -c "import openslide"
28 lines
1.3 KiB
Plaintext
28 lines
1.3 KiB
Plaintext
# Copy this file to .env and fill in your credentials
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# The .env file will be baked into the Docker image during build
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# Required for Claude Code if not using via subscription.
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ANTHROPIC_API_KEY=your_anthropic_api_key_here
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# Optional: Twilio credentials for SMS notifications
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TWILIO_ACCOUNT_SID=your_twilio_account_sid
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TWILIO_AUTH_TOKEN=your_twilio_auth_token
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TWILIO_FROM_NUMBER=+1234567890
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TWILIO_TO_NUMBER=+0987654321
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# Optional: Custom conda installation (for academic/lab environments)
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# Example: CONDA_PREFIX=/vol/biomedic3/username/miniconda3
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CONDA_PREFIX=
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# Optional: Additional conda directories (space-separated list)
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# Directories are mounted to the same path inside the container
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# Automatic detection:
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# - Paths with "*env*" are added to CONDA_ENVS_DIRS (for environments)
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# - Paths with "*pkg*" are added to CONDA_PKGS_DIRS (for package cache)
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# Example: CONDA_EXTRA_DIRS="/vol/biomedic3/username/.conda/envs /vol/biomedic3/username/conda_envs /vol/biomedic3/username/.conda/pkgs /vol/biomedic3/username/conda_pkgs /homes/username/.conda/envs"
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CONDA_EXTRA_DIRS=
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# Optional: System packages to install in Docker container (space-separated)
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# Common scientific packages: libopenslide0 libgdal-dev libproj-dev libopencv-dev
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# Example: SYSTEM_PACKAGES="libopenslide0 libgdal-dev"
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SYSTEM_PACKAGES= |