feat: Add Dockerfile for setting up PoseBench environment with dependencies

Author: amorehead

Dockerfile

@@ -0,0 +1,53 @@
+ARG PYTORCH_TAG=2.3.0-cuda11.8-cudnn8-devel
+FROM pytorch/pytorch:${PYTORCH_TAG}
+
+# Add system dependencies
+RUN apt-get update \
+    # Update image
+    && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
+        software-properties-common \
+        curl \
+        gnupg \
+    && echo "deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy main" > /etc/apt/sources.list.d/ubuntu-toolchain-r-test.list \
+    && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1E9377A2BA9EF27F \
+    && apt-get update \
+    # Install essential dependencies
+    && apt-get install --no-install-recommends -y \
+        build-essential \
+        git \
+        wget \
+        libxrender1 \
+        libxtst6 \
+        libxext6 \
+        libxi6 \
+        kalign \
+        gcc-11 \
+        g++-11 \
+    # Install Git LFS
+    && curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash \
+    && apt-get install --no-install-recommends -y git-lfs \
+    && git lfs install \
+    # Configure gcc/g++ versions
+    && update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100 \
+    && update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 100 \
+    # Clean up dependencies
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get autoremove -y \
+    && apt-get clean
+
+# Install Conda dependencies
+RUN conda install -y -c conda-forge python=3.10 gcc=11.4.0 gxx=11.4.0 libstdcxx=14.1.0 libstdcxx-ng=14.1.0 libgcc=14.1.0 libgcc-ng=14.1.0 compilers=1.5.2 libconeangle=0.1.1 pybind11=3.0.0 && \
+    conda clean -afy
+
+# Set work directory
+WORKDIR /app/posebench
+
+# Clone and install the package + requirements
+ARG GIT_TAG=main
+RUN git clone https://github.com/BioinfoMachineLearning/posebench . --branch ${GIT_TAG} \
+    && conda env update -f environments/posebench_environment.yaml \
+    && pip install -e . \
+    && pip install numpy==1.26.4 --no-dependencies \
+    && pip install prody==2.4.1 --no-dependencies \
+    && conda clean -afy \
+    && rm -rf /root/.cache/pip