Dockerfile

FROM ubuntu:xenial

# for easy upgrade later. ARG variables only persist during image build
ARG SAMTOOLSVER=1.14

LABEL base.image="ubuntu:xenial"
LABEL dockerfile.version="1"
LABEL software="Samtools"
LABEL software.version="1.14"
LABEL description="Tools (written in C using htslib) for manipulating next-generation sequencing data"
LABEL website="https://github.com/samtools/samtools"
LABEL license="https://github.com/samtools/samtools/blob/develop/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="eriny@utah.gov"
LABEL maintainer2="Curtis Kapsak"
LABEL maintainer2.email="kapsakcj@gmail.com"

# install dependencies and clean up apt garbage
RUN apt-get update && apt-get install --no-install-recommends -y \
 libncurses5-dev \
 libbz2-dev \
 liblzma-dev \
 libcurl4-gnutls-dev \
 zlib1g-dev \
 libssl-dev \
 gcc \
 wget \
 make \
 perl \
 bzip2 \
 gnuplot \
 ca-certificates \
 gawk && \
 apt-get autoclean && rm -rf /var/lib/apt/lists/*

# install samtools, make /data
RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \
 tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \
 rm samtools-${SAMTOOLSVER}.tar.bz2 && \
 cd samtools-${SAMTOOLSVER} && \
 ./configure && \
 make && \
 make install && \
 mkdir /data

# set perl locale settings
ENV LC_ALL=C

WORKDIR /data