--- a +++ b/Dockerfile @@ -0,0 +1,44 @@ +FROM dabinjeong/cuda:10.1-cudnn7-devel-ubuntu18.04 + +LABEL maintainer="Dabin Jeong" + +ENV TZ=Asia/Seoul +ENV DEBCONF_NOWARNINGS yes +ENV DEBIAN_FRONTEND=noninteractive + +RUN apt-get update && apt-get install -y apt-utils && apt-get install -y wget +RUN apt-get install -y libzmq3-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev build-essential libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev +## install R +RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/" >> /etc/apt/sources.list +RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc +RUN apt-get update +RUN apt-get install -y r-base +RUN Rscript -e "if (!require('BiocManager', quietly = TRUE)) install.packages('BiocManager')" +RUN Rscript -e "install.packages('argparse', dependencies = TRUE)" +RUN Rscript -e "install.packages('tidyverse',dependencies = TRUE)" +RUN PATH=/usr/bin/R:$PATH;export PATH + +### Install miniconda +ENV PATH /opt/conda/bin:$PATH +RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh -O /tmp/miniconda.sh && \ + echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \ + /bin/bash /tmp/miniconda.sh -b -p /opt/conda && \ + rm -rf /tmp/* + +RUN conda update -n base -c defaults conda + +ADD ./environment.yml . +RUN conda env update --file ./environment.yml &&\ + conda clean -tipy + +RUN conda init bash + +## Install torch, torch-geometric +RUN pip install torch==1.8.1+cu101 torchvision==0.9.1+cu101 torchaudio==0.8.1 -f https://download.pytorch.org/whl/torch_stable.html +RUN pip install torch-scatter torch-sparse==0.6.12 -f https://data.pyg.org/whl/torch-1.8.1+cu101.html +RUN pip install torch-geometric==2.2 + +COPY modules/* /tools/ + +ENTRYPOINT ["/usr/bin/env"] +CMD ["/bin/bash"]