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adding version 1.19 for samtools/bcftools/htslib (#830)
* adding version 1.19 * added plugins * added list plugins * Update README.md fix internal bcftools links --------- Co-authored-by: Kutluhan Incekara <[email protected]>
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| # for easy upgrade later. ARG variables only persist during build time | ||
| ARG BCFTOOLS_VER="1.19" | ||
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| FROM ubuntu:jammy as builder | ||
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| # re-instantiate variable | ||
| ARG BCFTOOLS_VER | ||
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| # 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 | ||
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| # 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-${BCFTOOLS_VER} && \ | ||
| make && \ | ||
| make install && \ | ||
| make test | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy as app | ||
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| # re-instantiate variable | ||
| ARG BCFTOOLS_VER | ||
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| # putting the labels in | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="bcftools" | ||
| LABEL software.version="${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]" | ||
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| # 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 | ||
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| WORKDIR /bcftools/plugins | ||
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| # 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 | ||
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| # set locale settings for singularity compatibility | ||
| ENV LC_ALL=C BCFTOOLS_PLUGINS='/bcftools/plugins' | ||
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| # set final working directory | ||
| WORKDIR /data | ||
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| # default command is to pull up help optoins | ||
| CMD ["bcftools", "--help"] | ||
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| ### start of test stage ### | ||
| FROM app as test | ||
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| # running --help and listing plugins | ||
| RUN bcftools --help && bcftools plugin -lv | ||
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| # install wget for downloading test files | ||
| RUN apt-get update && apt-get install --no-install-recommends -y wget ca-certificates | ||
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| 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 | ||
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| # 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 |
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| # bcftools container | ||
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| Main tool: | ||
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| * [https://www.htslib.org/](https://www.htslib.org/) | ||
| * [GitHub](https://github.com/samtools/bcftools) | ||
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| Additional tools: | ||
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| * perl 5.34.0 | ||
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| ## Example Usage | ||
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| ```bash | ||
| bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf | ||
| ``` | ||
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| Better documentation can be found at [https://www.htslib.org/doc/bcftools.html](https://www.htslib.org/doc/bcftools.html) |
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| # for easy upgrade later. ARG variables only persist during build time | ||
| ARG HTSLIB_VER="1.19" | ||
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| FROM ubuntu:jammy as builder | ||
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| ARG HTSLIB_VER | ||
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| # install dependencies, cleanup apt garbage | ||
| # It's helpful when they're all listed on https://github.com/samtools/htslib/blob/develop/INSTALL | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| wget \ | ||
| ca-certificates \ | ||
| make \ | ||
| bzip2 \ | ||
| autoconf \ | ||
| automake \ | ||
| make \ | ||
| gcc \ | ||
| perl \ | ||
| zlib1g-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| libssl-dev \ | ||
| procps && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| # get htslib, compile, install, run test suite | ||
| RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| tar -vxjf htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| rm -v htslib-${HTSLIB_VER}.tar.bz2 && \ | ||
| cd htslib-${HTSLIB_VER} && \ | ||
| make && \ | ||
| make install && \ | ||
| make test | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy as app | ||
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| ARG HTSLIB_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="htslib" | ||
| LABEL software.version="${HTSLIB_VER}" | ||
| LABEL description="A C library for reading/writing high-throughput sequencing data" | ||
| LABEL website="https://github.com/samtools/htslib" | ||
| LABEL license="https://github.com/samtools/htslib/blob/develop/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Curtis Kapsak" | ||
| LABEL maintainer2.email="[email protected]" | ||
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| # install runtime dependencies & cleanup apt garbage | ||
| # installed as recommend here: https://github.com/samtools/htslib/blob/develop/INSTALL#L31 | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| bzip2 \ | ||
| zlib1g-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| ca-certificates \ | ||
| && apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
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| # copy in htslib executables from builder stage | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
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| # set locale settings for singularity compatibility | ||
| ENV LC_ALL=C | ||
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| # set working directory | ||
| WORKDIR /data | ||
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| # default command is to show help options | ||
| CMD ["htsfile", "--help"] | ||
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| ### start of test stage ### | ||
| FROM app as test | ||
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| # check that these three executables are available | ||
| RUN bgzip --help && tabix --help && htsfile --help | ||
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| # FYI Test suite "make test" now performed in the builder stage since app and | ||
| # test stages do not include htslib source code. | ||
| # This is to avoid having to re-download source code simply to run test suite |
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| # htslib container | ||
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| Main tool: | ||
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| * [https://www.htslib.org/](https://www.htslib.org/) | ||
| * [GitHub](https://github.com/samtools/htslib) | ||
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| Additional tools: | ||
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| * perl 5.34.0 | ||
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| ## Example Usage | ||
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| ```bash | ||
| # determine file formats for various BAM and SAM files | ||
| $ htsfile tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam | ||
| tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam: BAM version 1 compressed sequence data | ||
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| $ htsfile ce_tag_padded.sam | ||
| ce_tag_padded.sam: SAM version 1.4 sequence text | ||
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| # compresses sample.fastq to sample.fastq.gz in BGZF format (blocked GNU Zip Format) | ||
| $ bgzip sample.fastq | ||
| ``` | ||
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| Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html) |
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| Original file line number | Diff line number | Diff line change |
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| ARG SAMTOOLS_VER="1.19" | ||
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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 \ | ||
| gcc \ | ||
| wget \ | ||
| make \ | ||
| perl \ | ||
| bzip2 \ | ||
| gnuplot \ | ||
| ca-certificates | ||
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| # download, compile, and install samtools | ||
| 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 | ||
|
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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 \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| 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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| # install wget for downloading test files | ||
| RUN apt-get update && apt-get install --no-install-recommends -y wget ca-certificates | ||
|
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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: | ||
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| * [https://www.htslib.org/](https://www.htslib.org/) | ||
| * [GitHub](https://github.com/samtools/samtools) | ||
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| Additional tools: | ||
|
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| * perl 5.34.0 | ||
|
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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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| Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html) |