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| ARG SAMTOOLS_VER="1.21" | ||
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| FROM ubuntu:jammy as builder | ||
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| ARG SAMTOOLS_VER | ||
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| # install dependencies required for compiling samtools | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| libncurses5-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| zlib1g-dev \ | ||
| libssl-dev \ | ||
| libdeflate-dev \ | ||
| gcc \ | ||
| wget \ | ||
| make \ | ||
| perl \ | ||
| bzip2 \ | ||
| gnuplot \ | ||
| ca-certificates | ||
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| # download, compile, and install samtools | ||
| RUN wget -q 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 && \ | ||
| make test | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy as app | ||
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| ARG SAMTOOLS_VER | ||
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| 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="[email protected]" | ||
| LABEL maintainer2="Curtis Kapsak" | ||
| LABEL maintainer2.email="[email protected]" | ||
| LABEL maintainer3="Erin Young" | ||
| LABEL maintainer3.email="[email protected]" | ||
| LABEL maintainer4="Kutluhan Incekara" | ||
| LABEL maintainer4.email="[email protected]" | ||
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| ARG DEBIAN_FRONTEND=noninteractive | ||
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| # install dependencies required for running samtools | ||
| # 'gnuplot' required for plot-ampliconstats | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| perl \ | ||
| zlib1g \ | ||
| libncurses5 \ | ||
| bzip2 \ | ||
| liblzma5 \ | ||
| libcurl3-gnutls \ | ||
| libdeflate0 \ | ||
| gnuplot \ | ||
| && apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # copy in samtools executables from builder stage | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
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| ENV LC_ALL=C | ||
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| # final working directory is /data | ||
| WORKDIR /data | ||
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| # default command is to pull up help options | ||
| CMD ["samtools", "--help"] | ||
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| ### start of test stage ### | ||
| FROM app as test | ||
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| ARG SAMTOOLS_VER | ||
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| # check PATH | ||
| RUN samtools --help | ||
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| # install make and wget for downloading test files | ||
| RUN apt-get update && apt-get install --no-install-recommends -y wget ca-certificates | ||
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| WORKDIR /test | ||
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| RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \ | ||
| wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam && \ | ||
| wget -q https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed && \ | ||
| samtools stats SRR13957123.primertrim.sorted.bam && \ | ||
| samtools faidx SRR13957123.consensus.fa && \ | ||
| samtools ampliconstats nCoV-2019.primer.bed SRR13957123.primertrim.sorted.bam > SRR13957123_ampliconstats.txt && \ | ||
| plot-ampliconstats plot SRR13957123_ampliconstats.txt && \ | ||
| ls |
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| # samtools container | ||
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| Main tool: [samtools](https://www.htslib.org/) | ||
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| Code repository: https://github.com/samtools/samtools | ||
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| Additional tools: | ||
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| * perl 5.34.0 | ||
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| Basic information on how to use this tool: | ||
| - executable: samtools | ||
| - help: --help | ||
| - version: --version | ||
| - description: Utilities for the Sequence Alignment/Map (SAM) format | ||
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| Additional information: | ||
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| This container includes samtools v1.20 compiled with **libdeflate** for a better cloud performance. | ||
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| Full documentation: https://www.htslib.org/doc/samtools.html | ||
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| ## Example Usage | ||
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| ```bash | ||
| samtools ampliconclip -b bed.file input.bam | ||
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| samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam | ||
| ``` | ||
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