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Merge pull request #778 from Kincekara/ki-bracken
add bracken
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| ARG KRAKEN_VER="2.1.3" | ||
| ARG BRACKEN_VER="2.9" | ||
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| ## Builder ## | ||
| FROM ubuntu:jammy as builder | ||
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| ARG KRAKEN_VER | ||
| ARG BRACKEN_VER | ||
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| RUN apt-get update && apt-get install -y build-essential perl wget zlib1g-dev | ||
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| # install Kraken2 | ||
| RUN wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v${KRAKEN_VER}.tar.gz &&\ | ||
| tar -xvf v${KRAKEN_VER}.tar.gz &&\ | ||
| cd kraken2-${KRAKEN_VER} &&\ | ||
| ./install_kraken2.sh /kraken2 | ||
| # install Bracken | ||
| RUN wget https://github.com/jenniferlu717/Bracken/archive/refs/tags/v${BRACKEN_VER}.tar.gz &&\ | ||
| tar -xvf v${BRACKEN_VER}.tar.gz && rm v${BRACKEN_VER}.tar.gz &&\ | ||
| cd Bracken-${BRACKEN_VER} &&\ | ||
| chmod 755 install_bracken.sh && ./install_bracken.sh | ||
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| ## App ## | ||
| FROM ubuntu:jammy as app | ||
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| ARG BRACKEN_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Bracken" | ||
| LABEL software.version=${BRACKEN_VER} | ||
| LABEL description="Bracken: estimating species abundance in metagenomics data" | ||
| LABEL website="https://github.com/jenniferlu717/Bracken" | ||
| LABEL license="https://github.com/jenniferlu717/Bracken/blob/master/LICENSE" | ||
| LABEL maintainer="Kutluhan Incekara" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y perl python-is-python3 libgomp1 pigz \ | ||
| && rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| COPY --from=builder /kraken2 /kraken2 | ||
| COPY --from=builder /Bracken-${BRACKEN_VER} /Bracken | ||
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| ENV LC_ALL=C | ||
| ENV PATH="${PATH}:/kraken2:/Bracken" | ||
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| CMD [ "bracken", "-h" ] | ||
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| WORKDIR /data | ||
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| ## Test ## | ||
| FROM app as test | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y wget | ||
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| # get kraken/bracken database | ||
| RUN wget --no-check-certificate https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20231009.tar.gz && \ | ||
| mkdir db && tar -C db -xvf k2_viral_20231009.tar.gz | ||
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| # download and classify SARS-CoV-2 reads | ||
| RUN wget --no-check-certificate https://github.com/StaPH-B/docker-builds/raw/83ee344304794f4ffa162d1c082bb35f916badcf/tests/SARS-CoV-2/SRR13957123_1.fastq.gz \ | ||
| https://github.com/StaPH-B/docker-builds/raw/83ee344304794f4ffa162d1c082bb35f916badcf/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \ | ||
| kraken2 --db ./db --paired --report k2_report.txt SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz | ||
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| # make abundance estimation with bracken | ||
| RUN bracken -d ./db -i k2_report.txt -o bracken_report.txt -r 75 -l S -t 10 && \ | ||
| cat bracken_report.txt |
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| # Bracken container | ||
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| Main tool: [Bracken](https://github.com/jenniferlu717/Bracken) | ||
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| Code repository: https://github.com/jenniferlu717/Bracken | ||
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| Additional tools: | ||
| - kraken2: 2.1.3 | ||
| - python: 3.10.12 | ||
| - perl: 5.34.0 | ||
| - pigz: 2.6 | ||
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| Basic information on how to use this tool: | ||
| - executable: bracken | ||
| - help: -h | ||
| - version: -v | ||
| - description: Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). | ||
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| Additional information: | ||
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| This container does not contain any kraken or bracken database. Please download precompiled database from [Ben Langmead's page](https://benlangmead.github.io/aws-indexes/k2). Those database files includes both kraken2 and bracken indexes. | ||
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| Full documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual | ||
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| ## Example Usage | ||
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| ```bash | ||
| bracken -d database_folder -i kraken_report -o bracken_report -r 75 -l S -t 10 | ||
| ``` |