Dockerfile

# builder
FROM ubuntu:jammy as builder

ARG SAMTOOLS_VER="1.17"

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

RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
    tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
    cd samtools-${SAMTOOLS_VER} && \
    ./configure && \
    make && \
    make install

# app
FROM ubuntu:jammy as app

ARG SAMTOOLS_VER="1.17"

LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="Samtools"
LABEL software.version="${SAMTOOLS_VER}"
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="Shelby Bennett"
LABEL maintainer.email="shelby.bennett@dgs.virginia.gov"
LABEL maintainer2="Kutluhan Incekara"
LABEL maintainer2.email="kutluhan.incekara@ct.gov"

RUN apt-get update && apt-get install --no-install-recommends -y \
    perl \
    zlib1g \
    libncurses5 \
    bzip2 \
    liblzma-dev \
    libcurl4-gnutls-dev \
    && apt-get autoclean && rm -rf /var/lib/apt/lists/*

COPY --from=builder /usr/local/bin/* /usr/local/bin/ 

ENV LC_ALL=C

WORKDIR /data

# test
FROM app as test

RUN apt-get update && apt-get install -y wget &&\
    wget https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
    wget https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam && \
    samtools stats SRR13957123.primertrim.sorted.bam && \
    samtools faidx SRR13957123.consensus.fa