Basic Dockerfile for fully-featured HTSlib/SAMtools/BCFtools

Dockerfile

ARG  ubuntu_version=latest
FROM ubuntu:${ubuntu_version}

USER root

RUN apt-get update && apt-get install -y \
	build-essential \
	curl \
	git \
	libbz2-dev \
	libcurl4-openssl-dev \
	libgsl0-dev \
	liblzma-dev \
	libncurses5-dev \
	libperl-dev \
	libssl-dev \
	zlib1g-dev \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /tmp
ARG htsversion=1.9
RUN curl -L https://github.com/samtools/htslib/releases/download/${htsversion}/htslib-${htsversion}.tar.bz2 | tar xj && \
    (cd htslib-${htsversion} && ./configure --enable-plugins --with-plugin-path='$(libexecdir)/htslib:/usr/libexec/htslib' && make install) && \
    ldconfig && \
    curl -L https://github.com/samtools/samtools/releases/download/${htsversion}/samtools-${htsversion}.tar.bz2 | tar xj && \
    (cd samtools-${htsversion} && ./configure --with-htslib=system && make install) && \
    curl -L https://github.com/samtools/bcftools/releases/download/${htsversion}/bcftools-${htsversion}.tar.bz2 | tar xj && \
    (cd bcftools-${htsversion} && ./configure --enable-libgsl --enable-perl-filters --with-htslib=system && make install) && \
    git clone --depth 1 git://github.com/samtools/htslib-plugins && \
    (cd htslib-plugins && make PLUGINS='hfile_cip.so hfile_mmap.so' install)