Dockerfile

FROM ubuntu:20.04
MAINTAINER jmonlong@ucsc.edu

# Prevent dpkg from trying to ask any questions, ever
ENV DEBIAN_FRONTEND noninteractive
ENV DEBCONF_NONINTERACTIVE_SEEN true

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    wget \
    git \
    gcc \
    make \
    bzip2 \
    tabix \
    r-base r-base-dev \
    libxml2-dev \
    libssl-dev \
    libmariadbclient-dev \
    libcurl4-openssl-dev \
    apt-transport-https \
    software-properties-common \
    dirmngr \
    gpg-agent \
    libncurses5-dev \
    libncursesw5-dev \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    && rm -rf /var/lib/apt/lists/*

## R with sveval package
ADD . /sveval

WORKDIR /sveval

RUN R -f install.R

## bcftools
RUN wget --no-check-certificate https://github.com/samtools/bcftools/releases/download/1.17/bcftools-1.17.tar.bz2 && \
        tar -xjf bcftools-1.17.tar.bz2 && \
        cd bcftools-1.17 && \
        ./configure && make && make install && \
        cd .. && rm -rf bcftools-1.17.tar.bz2

## Dependencies
RUN apt-get update \
        && apt-get install -y --no-install-recommends \
        wget \
        git \
        curl \
        python3 \
        python3-dev \
        python3-pip \
        python3-setuptools \
        tabix \
        && rm -rf /var/lib/apt/lists/*

## Install snakemake
RUN pip3 install --upgrade pip
RUN pip3 install --no-cache-dir snakemake==7.29.0

RUN mkdir /.cache; chmod a+rwX /.cache

WORKDIR /home