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* updating htslib to 1.21 * Update README.md v.1.20 -> v.1.21 --------- Co-authored-by: Kutluhan Incekara <[email protected]>
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| # for easy upgrade later. ARG variables only persist during build time | ||
| ARG HTSLIB_VER="1.21" | ||
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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 \ | ||
| libdeflate-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-${HTSLIB_VER} && \ | ||
| ./configure && \ | ||
| make && \ | ||
| make install && \ | ||
| make test | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy as app | ||
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| ARG HTSLIB_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="htslib" | ||
| LABEL software.version="${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 \ | ||
| libbz2-1.0 \ | ||
| liblzma5 \ | ||
| libcurl3-gnutls \ | ||
| libdeflate0 \ | ||
| 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/ | ||
| COPY --from=builder /usr/local/lib/ /usr/local/lib/ | ||
| COPY --from=builder /usr/local/include/ /usr/local/include/ | ||
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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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| RUN apt-get update && apt-get install --no-install-recommends -y wget | ||
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| # use on actual files | ||
| RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ | ||
| gunzip SRR13957123_1.fastq.gz && \ | ||
| bgzip SRR13957123_1.fastq | ||
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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: [htslib](https://www.htslib.org/) | ||
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| Code repository: https://github.com/samtools/htslib | ||
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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: htsfile | ||
| - help: --help | ||
| - version: --version | ||
| - description: The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file. | ||
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| Additional information: | ||
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| This container includes htslib v1.21 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 | ||
| # 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 | ||
| ``` |