diff --git a/Dockerfile b/Dockerfile index 4afb414ff6f86ca0efb9d1c511d629bc666ffabd..2b70c668727907c03dd0ce1986317acd33e89ce1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,3 +1,77 @@ +# Use the official Anaconda base image FROM continuumio/anaconda3 -RUN apt-get update && apt-get install -y libgl1 \ No newline at end of file +# Set environment variable to avoid user interaction during package installation +ENV DEBIAN_FRONTEND=noninteractive + +## Update package list and install necessary packages for X11, Qt, and basic utilities +#RUN apt-get update && \ +# apt-get install -y \ +# x11-apps \ +# xauth \ +# libx11-dev \ +# libxext6 \ +# libxrender1 \ +# libxrandr2 \ +# libxfixes3 \ +# libxi6 \ +# libxkbcommon-x11-0 \ +# libgl1-mesa-glx \ +# libqt5widgets5 \ +# libqt5gui5 \ +# libqt5core5a \ +# fonts-dejavu-core \ +# pciutils \ +# make \ +# less \ +# nano \ +# && apt-get clean && \ +# rm -rf /var/lib/apt/lists/* + +RUN apt-get update && \ + apt-get install -y \ + less \ + nano \ + && apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +RUN useradd -ms /bin/bash clarkad + +# Set environment variables for X11 forwarding and Qt plugins +#ENV DISPLAY=:0 +#ENV QT_QPA_PLATFORM=xcb +#ENV QT_PLUGIN_PATH=/usr/lib/x86_64-linux-gnu/qt5/plugins + +RUN conda create -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython + +# Ensure conda is initialized in every new shell +#RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> /opt/.bashrc +#RUN echo "conda activate spyder-env" >> /opt/.bashrc + +##----------------------------------------------------------------------------## +## Install parallel +##----------------------------------------------------------------------------## + +#WORKDIR /opt +#COPY ./parallel.tar.bz2 /opt +#RUN tar -xjf parallel.tar.bz2 +# +#WORKDIR /opt/parallel-20240322 +## build and install +#RUN ./configure && make && make install +# +#WORKDIR /opt +## verify version of parallel installed +#RUN parallel --version | head -1 +## get past annoying parallel citation prompt +#RUN echo 'will cite' | parallel --citation &> /dev/null || true + +#COPY ./cellxgene.txt /opt +#RUN conda create -n cellxgene --file /opt/cellxgene.txt +#RUN echo "conda activate cellxgene" >> /opt/.bashrc + +ADD cxg_env.yml /tmp/cxg_env.yml +RUN conda env create -f /tmp/cxg_env.yml + +SHELL ["bash"] +ENTRYPOINT [ "conda", "run", "--no-capture-output", "-n", "spyder-env", "spyder" ] \ No newline at end of file