Upload Dockerfile to examples (#222)

* Upload Dockerfile to examples

* Update Foundry README with Docker information

- There is an image for Foundry on DockerHub
- Example recipe is in `foundry/examples/docker`

---------

Co-authored-by: Rachel Clune <rachel.clune@omsf.io>

Author: woodsh17

README.md

@@ -41,6 +41,14 @@ foundry list-installed
 
 >*See `examples/all.ipynb` for how to run each model and design proteins end-to-end in a notebook.*
 
+### Docker Image
+
+There is an official [Foundry image](https://hub.docker.com/r/rosettacommons/foundry) maintained by the [Rosetta Commons](https://rosettacommons.org/). The default image comes with the model weights for the available models, but you can use the `slim` tag to either use pre-exiting model weights or use the image to download the available model weights. 
+
+For more information and example syntax, see the [Overview on DockerHub](https://hub.docker.com/r/rosettacommons/foundry).
+
+The recipe to create the Docker image can be found in `foundry/examples/docker` and can be used as a "blue-print" for creating your own images. 
+
 ### Google Colab
 For an interactive Google Colab notebook walking through a basic design pipeline with RFD3, MPNN, and RF3, please see the [IPD Design Pipeline Tutorial](https://colab.research.google.com/drive/1ZwIMV3n9h0ZOnIXX0GyKUuoiahgifBxh?usp=sharing).
 

examples/docker/Dockerfile

@@ -0,0 +1,65 @@
+# Base image reference:
+# The official Foundry Docker image hosted by Rosetta Commons is available at:
+# https://hub.docker.com/r/rosettacommons/foundry
+#
+# This Dockerfile serves as a reference starting point for building a custom
+# Foundry image. You may optionally exclude checkpoint file downloads to
+# reduce the final image size.
+#
+# Authors:
+# Hope Woods <hope.woods@omsf.io>
+# Rachel Clune <rachel.clune@omsf.io>
+# Sergey Lyskov <sergey.lyskov@gmail.com>
+
+ARG BASE_IMAGE=ubuntu:22.04
+FROM ${BASE_IMAGE} AS BUILDER
+
+COPY --from=ghcr.io/astral-sh/uv /uv /uvx /bin/
+
+# Install system dependencies and build tools
+RUN apt-get update && apt-get install -y --no-install-recommends \
+     ca-certificates \
+     git \
+     mc \
+     build-essential \
+     && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Set up app directory and user
+WORKDIR /app
+
+# Create a virtual environment and install dependencies with uv
+RUN git clone https://github.com/RosettaCommons/foundry /app/foundry \
+    && cd /app/foundry \
+    && uv venv --python 3.12 \
+    && uv pip install ".[all]" \
+    && /app/foundry/.venv/bin/foundry --help \
+    && /app/foundry/.venv/bin/foundry install base-models --checkpoint-dir /app/foundry/checkpoints \
+    && uv cache clean \
+    && chmod -R a+rX /root \
+    && chmod -R a+rX /app \
+    && echo
+
+#FINAL -------------------------------------------------------------------
+FROM ${BASE_IMAGE}
+
+COPY --from=BUILDER /root /root
+COPY --from=BUILDER /app /app
+RUN chmod -R a+rX /root && chmod -R a+rX /app
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    mc \
+    build-essential \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Activate the venv at container start
+ENV PATH="/app/foundry/.venv/bin:$PATH"
+WORKDIR /app/foundry
+
+# Use bash as default shell
+SHELL ["/bin/bash", "-c"]
+
+# Do not set a default command to run foundry since each models uses a different command
+CMD ["bash"]
+