Dockerfile

FROM hpcaitech/pytorch-cuda:1.12.0-11.3.0

RUN conda install openmm=7.7.0 pdbfixer -c conda-forge -y \
 && conda install hmmer==3.3.2 hhsuite=3.3.0 kalign2=2.04 -c bioconda -y

RUN pip install biopython==1.79 dm-tree==0.1.6 ml-collections==0.1.0 \
scipy==1.7.1 ray pyarrow pandas einops

RUN pip install colossalai==0.1.10+torch1.12cu11.3 -f https://release.colossalai.org

RUN git clone https://github.com/openai/triton.git ~/triton \
 && cd ~/triton/python \
 && pip install -e .

Run git clone https://github.com/hpcaitech/FastFold.git \
 && cd ./FastFold \
 && python setup.py install