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adding bcftools version 1.21 (#1055)
* adding bcftools version 1.21 * Update README.md changed v1.20 to 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 BCFTOOLS_VER="1.21" | ||
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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 \ | ||
| libdeflate-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-${BCFTOOLS_VER} && \ | ||
| ./configure --enable-libgsl --enable-perl-filters &&\ | ||
| make && \ | ||
| make install && \ | ||
| make test | ||
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| ### start of app stage ### | ||
| FROM ubuntu:jammy as app | ||
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| # re-instantiate variable | ||
| ARG BCFTOOLS_VER | ||
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| # putting the labels in | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="bcftools" | ||
| LABEL software.version="${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 \ | ||
| gsl-bin \ | ||
| bzip2 \ | ||
| liblzma5 \ | ||
| libcurl3-gnutls \ | ||
| libdeflate0 \ | ||
| procps \ | ||
| && apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # copy in bcftools executables from builder stage | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
| # copy in bcftools plugins from builder stage | ||
| COPY --from=builder /usr/local/libexec/bcftools/* /usr/local/libexec/bcftools/ | ||
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| # set locale settings for singularity compatibility | ||
| ENV LC_ALL=C | ||
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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 -y wget vcftools | ||
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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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| RUN echo "testing plugins..." && \ | ||
| bcftools +counts SRR13957123.vcf | ||
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| RUN echo "testing polysomy..." && \ | ||
| wget https://samtools.github.io/bcftools/howtos/cnv-calling/usage-example.tgz &&\ | ||
| tar -xvf usage-example.tgz &&\ | ||
| zcat test.fcr.gz | ./fcr-to-vcf -b bcftools -a map.tab.gz -o outdir/ &&\ | ||
| bcftools cnv -o cnv/ outdir/test.vcf.gz &&\ | ||
| bcftools polysomy -o psmy/ outdir/test.vcf.gz &&\ | ||
| head psmy/dist.dat | ||
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| RUN echo "reading test data from Google Cloud to validate GCS support" && \ | ||
| bcftools head -h 20 gs://genomics-public-data/references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz | ||
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| RUN echo "reading test data from S3 to validate AWS support" && \ | ||
| bcftools head -h 20 s3://human-pangenomics/T2T/CHM13/assemblies/variants/GATK_CHM13v2.0_Resource_Bundle/resources-broad-hg38-v0-1000G_phase1.snps.high_confidence.hg38.t2t-chm13-v2.0.vcf.gz |
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| # bcftools container | ||
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| Main tool: [bcftools](https://github.com/samtools/bcftools) | ||
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| Code repository: https://github.com/samtools/bcftools | ||
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| Basic information on how to use this tool: | ||
| - executable: bcftools | ||
| - help: --help | ||
| - version: --version | ||
| - description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. | ||
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| Additional information: | ||
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| This container includes bcftools v1.21 compiled with **libdeflate** for a better cloud performance. Also, "polysomy" and plugins are enabled in this image. | ||
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| Full documentation: https://samtools.github.io/bcftools/howtos/index.html | ||
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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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