Dockerfile

FROM buildpack-deps:artful

# Set up locales properly
RUN apt-get update && \
    apt-get install --yes --no-install-recommends locales && \
    apt-get purge && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
    locale-gen

ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8

# Use bash as default shell, rather than sh
ENV SHELL /bin/bash

# run critical system updates ... one could also use the artful-curl pack
RUN apt-get update && \
    apt-get install --yes --no-install-recommends \
        wget bzip2 ca-certificates curl git && \
    apt-get purge && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# install conda
ENV CONDA_FILE https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN echo "export PATH=/opt/conda/bin:$PATH" > /etc/profile.d/conda.sh && \
    wget --quiet ${CONDA_FILE} -O /tmp/miniconda.sh && \
    /bin/bash /tmp/miniconda.sh -b -p /opt/conda && \
    rm /tmp/miniconda.sh && \
    /opt/conda/bin/conda clean -tipsy
ENV PATH /opt/conda/bin:$PATH

# alternative conda install (instead of the manual install from above)
# FROM continuumio/miniconda3:latest

# set up a user, to avoid running containers as root
ENV NB_USER container_user
ENV HOME /home/${NB_USER}
RUN adduser --disabled-password \
    --gecos "Default user" \
    ${NB_USER}

# download things to tmp
WORKDIR /tmp

# download the conda environment OR copy from local directory
RUN wget --quiet https://raw.githubusercontent.com/letaylor/snakemake-qtl/master/environment.yml -O /tmp/environment.yml
#COPY environment.yml /tmp/environment.yml

# install conda environment
# NOTE: conda clean -tipsy
#   removes everything w/o confirmation (leaves all environments functional).
RUN conda update conda --yes && \
    #conda env create --name container_env --file environment.yml && \
    #conda list --name container_env && \
    #echo "source activate container_env" >> ${HOME}/.bashrc && \
    conda env update -v -n root --file /tmp/environment.yml && \
    conda list --name root && \
    #conda clean --all --yes && \
    conda clean -tipsy && \
    rm /tmp/environment.yml

# export the conda path to force container_env since .bashrc necessarily 
# sourced when when the image is used
# ENV PATH /opt/conda/envs/container_env/bin:$PATH
# ENV CONDA_DEFAULT_ENV container_env
# ENV CONDA_PREFIX /opt/conda/envs/container_env

# install QTLTools
RUN wget --quiet \
https://qtltools.github.io/qtltools/binaries/QTLtools_1.1_Ubuntu14.04_x86_64.tar.gz && \
    tar -zxvf \
        QTLtools_1.1_Ubuntu14.04_x86_64.tar.gz \
        QTLtools_1.1_Ubuntu14.04_x86_64 && \
    rm QTLtools_1.1_Ubuntu14.04_x86_64.tar.gz && \
    chmod 755 QTLtools_1.1_Ubuntu14.04_x86_64 && \
    mv QTLtools_1.1_Ubuntu14.04_x86_64 /bin/QTLtools

# install veqtl-mapper
RUN wget --quiet  https://github.com/funpopgen/veqtl-mapper/releases/download/1.02/veqtl-mapper && \
    chmod 755 veqtl-mapper && \
    mv veqtl-mapper /bin/veqtl-mapper

# set wd to user home
WORKDIR ${HOME}

# clear tmp if there is anything in there...
RUN rm -rf /tmp/*

# set bash as the default entry point
ENTRYPOINT [ "/bin/bash", "-c" ]

# set the user
USER ${NB_USER}