From 79c98a66d070949b760fda13b68cf06808f06be9 Mon Sep 17 00:00:00 2001 From: Young Date: Mon, 30 Sep 2024 06:49:22 -0600 Subject: [PATCH] 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 <46578029+Kincekara@users.noreply.github.com> --- README.md | 2 +- bcftools/1.21/Dockerfile | 117 +++++++++++++++++++++++++++++++++++++++ bcftools/1.21/README.md | 25 +++++++++ 3 files changed, 143 insertions(+), 1 deletion(-) create mode 100644 bcftools/1.21/Dockerfile create mode 100644 bcftools/1.21/README.md diff --git a/README.md b/README.md index d6a286024..2a031db91 100644 --- a/README.md +++ b/README.md @@ -124,7 +124,7 @@ To learn more about the docker pull rate limits and the open source software pro | [bakta](https://hub.docker.com/r/staphb/bakta)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | | https://github.com/oschwengers/bakta | | [bandage](https://hub.docker.com/r/staphb/bandage)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | | https://rrwick.github.io/Bandage/ | | [BBTools](https://hub.docker.com/r/staphb/bbtools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | | https://jgi.doe.gov/data-and-tools/bbtools/ | -| [bcftools](https://hub.docker.com/r/staphb/bcftools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | | https://github.com/samtools/bcftools | +| [bcftools](https://hub.docker.com/r/staphb/bcftools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | | https://github.com/samtools/bcftools | | [bedtools](https://hub.docker.com/r/staphb/bedtools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | | https://bedtools.readthedocs.io/en/latest/
https://github.com/arq5x/bedtools2 | | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | | none | | [blast+](https://hub.docker.com/r/staphb/blast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | | https://www.ncbi.nlm.nih.gov/books/NBK279690/ | diff --git a/bcftools/1.21/Dockerfile b/bcftools/1.21/Dockerfile new file mode 100644 index 000000000..7e14bc796 --- /dev/null +++ b/bcftools/1.21/Dockerfile @@ -0,0 +1,117 @@ +# for easy upgrade later. ARG variables only persist during build time +ARG BCFTOOLS_VER="1.21" + +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 \ + libdeflate-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-${BCFTOOLS_VER} && \ + ./configure --enable-libgsl --enable-perl-filters &&\ + make && \ + make install && \ + make test + +### start of app stage ### +FROM ubuntu:jammy as app + +# re-instantiate variable +ARG BCFTOOLS_VER + +# putting the labels in +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="bcftools" +LABEL software.version="${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="eriny@utah.gov" +LABEL maintainer2="Curtis Kapsak" +LABEL maintainer2.email="kapsakcj@gmail.com" + +# 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/* + +# 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/ + +# set locale settings for singularity compatibility +ENV LC_ALL=C + +# 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 -y wget vcftools + +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 + +RUN echo "testing plugins..." && \ + bcftools +counts SRR13957123.vcf + +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 + +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 + +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 diff --git a/bcftools/1.21/README.md b/bcftools/1.21/README.md new file mode 100644 index 000000000..005643cf1 --- /dev/null +++ b/bcftools/1.21/README.md @@ -0,0 +1,25 @@ +# bcftools container + +Main tool: [bcftools](https://github.com/samtools/bcftools) + +Code repository: https://github.com/samtools/bcftools + +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. + +Additional information: + +This container includes bcftools v1.21 compiled with **libdeflate** for a better cloud performance. Also, "polysomy" and plugins are enabled in this image. + +Full documentation: https://samtools.github.io/bcftools/howtos/index.html + +## Example Usage + +```bash +bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf +``` + +