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Commit f86d42f4 authored by Matthew W. Thompson's avatar Matthew W. Thompson
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Switch to Miniforge3

parent 6bf5c8ce
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View file @ f86d42f4
...@@ -13,24 +13,22 @@ RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/ ...@@ -13,24 +13,22 @@ RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/
RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
RUN wget -P /tmp \ RUN wget -P /tmp \
"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \ "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" \
&& bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \ && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
&& rm /tmp/Miniconda3-latest-Linux-x86_64.sh && rm /tmp/Miniforge3-Linux-x86_64.sh
ENV PATH /opt/conda/bin:$PATH ENV PATH /opt/conda/bin:$PATH
COPY environment.yml /opt/openfold/environment.yml COPY environment.yml /opt/openfold/environment.yml
# installing into the base environment since the docker container wont do anything other than run openfold # installing into the base environment since the docker container wont do anything other than run openfold
RUN conda env update -n base --file /opt/openfold/environment.yml && conda clean --all RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
COPY openfold /opt/openfold/openfold COPY openfold /opt/openfold/openfold
COPY scripts /opt/openfold/scripts COPY scripts /opt/openfold/scripts
COPY run_pretrained_openfold.py /opt/openfold/run_pretrained_openfold.py COPY run_pretrained_openfold.py /opt/openfold/run_pretrained_openfold.py
COPY train_openfold.py /opt/openfold/train_openfold.py COPY train_openfold.py /opt/openfold/train_openfold.py
COPY setup.py /opt/openfold/setup.py COPY setup.py /opt/openfold/setup.py
COPY lib/openmm.patch /opt/openfold/lib/openmm.patch
RUN wget -q -P /opt/openfold/openfold/resources \ RUN wget -q -P /opt/openfold/openfold/resources \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
RUN patch -p0 -d /opt/conda/lib/python3.9/site-packages/ < /opt/openfold/lib/openmm.patch
WORKDIR /opt/openfold WORKDIR /opt/openfold
RUN python3 setup.py install RUN python3 setup.py install
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