Dockerfile

FROM jupyter/datascience-notebook:a95cb64dfe10

MAINTAINER Melissa Gymrek <mgymrek@ucsd.edu>
USER root

# Install dependencies
RUN apt-get update && apt-get -qq install -y \
    cmake \
    datamash \
    default-jdk \
    git \
    less \
    libbz2-dev \
    liblzma-dev \
    libncurses5 libncurses5-dev \
    r-base \
    vim \
    zlib1g-dev

# Make sources directory
RUN mkdir /sources

# Install extra python packages
RUN pip install pyvcf

# Install nbgrader
RUN conda install nbgrader
RUN jupyter nbextension install --symlink --sys-prefix --py nbgrader
RUN jupyter nbextension enable --sys-prefix --py nbgrader
RUN jupyter serverextension enable --sys-prefix --py nbgrader

# disable formgrader, create-assignments for all. grader and assignment maker will run below with 'enable --user' instead of 'disable --sys-prefix'
RUN jupyter nbextension disable --sys-prefix formgrader/main --section=tree
RUN jupyter serverextension disable --sys-prefix nbgrader.server_extensions.formgrader
RUN jupyter nbextension disable --sys-prefix create_assignment/main

# Install course-specific software
ADD install_cse185_deps_wks1-3.sh /sources/
RUN chmod +x /sources/install_cse185_deps_wks1-3.sh
RUN /sources/install_cse185_deps_wks1-3.sh

ADD install_cse185_deps_wk4.sh /sources/
RUN chmod +x /sources/install_cse185_deps_wk4.sh
RUN /sources/install_cse185_deps_wk4.sh

ADD install_cse185_deps_wk5.sh /sources
RUN chmod +x /sources/install_cse185_deps_wk5.sh
RUN /sources/install_cse185_deps_wk5.sh

RUN rm /sources/*.tar.gz
RUN rm /sources/*.zip
RUN rm -rf /opt/julia
ADD install_cse185_deps_wk6.sh /sources
ADD cellranger-3.0.2.tar.gz /sources
RUN chmod +x /sources/install_cse185_deps_wk6.sh
RUN /sources/install_cse185_deps_wk6.sh
ENV PATH="${PATH}:/sources/cellranger-3.0.2"

# Set env variables
ENV PERL5LIB="${PERL5LIB}:/sources/sspace_basic/dotlib"
ENV PATH="${PATH}:/sources/homer/bin:/sources/meme-5.0.5/src/"