Reproducible Docker Environment with CREDO (Two-Stage Build)

This repository provides a fully reproducible and portable Docker environment built with CREDO.
The build process freezes all dependencies — both Python and R — into an immutable environment (/credo_env) that can be reapplied anywhere, ensuring determinism and portability.

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Build Overview

CREDO builds the environment in two stages:

1. Stage 1 – builder (Dockerfile.stage1)

   • Based on the official CREDO base image (ghcr.io/credoproject/core:v0.19.0-amd64).
   • Executes credo_install.sh, which reads requirements.txt and installs each tool using CREDO’s verbs (pip, cran, apt, github, etc.).
   • Saves the complete environment snapshot to /credo_env.

2. Stage 2 – final (Dockerfile.final)

   • Starts again from a clean CREDO base.
   • Copies the frozen /credo_env directory from the builder image.
   • Runs credo apply to materialize the same environment without network access, ensuring reproducibility.

This separation keeps the final image minimal and deterministic.

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File Overview

.
├── Dockerfile.stage1      # Builds the environment using CREDO
├── Dockerfile.final       # Applies the frozen environment for runtime
├── build_all.sh           # Automates the two-stage build
├── credo_install.sh       # Installs all tools declared in requirements.txt
└── requirements.txt       # Declarative list of software (CREDO syntax)

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How to Use

1. Edit requirements.txt
   Each line declares a package using CREDO verbs.
   Example:

   pip jupyterlab==4.2.5
   pip pandas==2.2.2
   pip numpy==2.0.1
   cran Seurat
   github fastai/fastcore@1.7.12
   

2. Run the full build process

   ./build_all.sh credotest

3. Run the final image

   docker run -it credotest

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Advantages

• Deterministic builds — the same input always yields the same environment.
• No network dependency in the final stage (credo apply uses only local artifacts).
• Cross-platform reproducibility — same environment works on Linux, macOS, and Windows (via Docker).
• Full transparency — inspect /credo_env to see every installed component.

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Windows Usage

Windows users can achieve the same reproducible build by running the preconfigured privileged Docker container that includes CREDO and Docker-in-Docker:

wun_credobuilder.cmd

This will:

1. Build the repbioinfo/credobuilder-dind image.
2. Clone the DockerBuilder helper repository if needed.
3. Start an interactive CREDO environment ready to run build_all.sh.