Dockerfile

# for easy upgrade later. ARG variables only persist during build time
ARG BCFTOOLS_VER="1.18"

FROM ubuntu:jammy as builder

# re-instantiate variable
ARG BCFTOOLS_VER

# install dependencies, cleanup apt garbage
RUN apt-get update && apt-get install --no-install-recommends -y \
  wget \
  ca-certificates \
  perl \
  bzip2 \
  autoconf \
  automake \
  make \
  gcc \
  zlib1g-dev \
  libbz2-dev \
  liblzma-dev \
  libcurl4-gnutls-dev \
  libssl-dev \
  libperl-dev \
  libgsl0-dev \
  procps && \
  rm -rf /var/lib/apt/lists/* && apt-get autoclean

# download, compile, and install bcftools
RUN wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VER}/bcftools-${BCFTOOLS_VER}.tar.bz2 && \
  tar -xjf bcftools-${BCFTOOLS_VER}.tar.bz2 && \
  rm -v bcftools-${BCFTOOLS_VER}.tar.bz2 && \
  cd bcftools-${BCFTOOLS_VER} && \
  make && \
  make install && \
  make test 

### start of app stage ###
FROM ubuntu:jammy as app

# re-instantiate variable
ARG BCFTOOLS_VER

# putting the labels in
LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="bcftools"
LABEL software.version="${BCFTOOLS_VER}"
LABEL description="Variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF"
LABEL website="https://github.com/samtools/bcftools"
LABEL license="https://github.com/samtools/bcftools/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 required for running bcftools
# https://github.com/samtools/bcftools/blob/develop/INSTALL#L29
RUN apt-get update && apt-get install --no-install-recommends -y \
    perl \
    zlib1g \
    libncurses5 \
    bzip2 \
    liblzma-dev \
    libcurl4-gnutls-dev \
    procps \
    && apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
    mkdir /data

# copy in bcftools executables from builder stage
COPY --from=builder /usr/local/bin/* /usr/local/bin/

# set locale settings for singularity compatibility
ENV LC_ALL=C

# set final working directory
WORKDIR /data

# default command is to pull up help optoins
CMD ["bcftools", "--help"]

### start of test stage ###
FROM app as test

# install wget for downloading test files
RUN apt-get update && apt-get install --no-install-recommends -y wget ca-certificates

RUN echo "downloading test SC2 BAM and FASTA and running bcftools mpileup and bcftools call test commands..." && \
  wget -q https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.reference.fasta && \
  wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam && \
  bcftools mpileup -A -d 200 -B -Q 0 -f SARS-CoV-2.reference.fasta SRR13957123.primertrim.sorted.bam | \
  bcftools call -mv -Ov -o SRR13957123.vcf

# FYI Test suite "make test" is performed in the builder stage since app and
# test stages do not include bcftools source code.
# This is to avoid having to re-download source code simply to run test suite