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Dockerfile
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# author Sergey Lyskov
# demo/reference Dockerfile for https://github.com/Graylab/MaskedProteinEnT repository
FROM python:3.10
RUN apt-get -y update
RUN apt-get -y install --no-install-recommends git curl
RUN git clone https://github.com/Graylab/MaskedProteinEnT.git /code
WORKDIR /code
RUN pip install torch torchvision torchaudio -f https://download.pytorch.org/whl/torch_stable.html
RUN pip install -r requirements.txt
RUN curl -O https://zenodo.org/records/8313466/files/model.tar.gz && tar -xvzf model.tar.gz && rm model.tar.gz
# testing if code working as expected
RUN python3 ProteinSequenceSampler.py \
--output_dir ./sampled_sequences \
--model models/ProtEnT_backup.ckpt \
--from_pdb data/proteins \
--sample_temperatures 0.2,0.5 \
--num_samples 100
RUN test -d ./sampled_sequences
RUN ls ./sampled_sequences
ENTRYPOINT /bin/bash