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Dockerfile
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# for easy upgrade later. ARG variables only persist during build time
ARG BCFTOOLS_VER="1.20"
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="[email protected]"
LABEL maintainer2="Curtis Kapsak"
LABEL maintainer2.email="[email protected]"
# 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
WORKDIR /bcftools/plugins
# copy in bcftools executables from builder stage
COPY --from=builder /usr/local/bin/* /usr/local/bin/
COPY --from=builder /bcftools-${BCFTOOLS_VER}/plugins/* /bcftools/plugins
# set locale settings for singularity compatibility
ENV LC_ALL=C BCFTOOLS_PLUGINS='/bcftools/plugins'
# 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
# running --help and listing plugins
RUN bcftools --help && bcftools plugin -lv
# 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