diff --git a/Program_Licenses.md b/Program_Licenses.md index bcd0c34d2..7bbd58481 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -17,6 +17,7 @@ The licenses of the open-source software that is contained in these Docker image | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE | | blast+ | Public Domain | https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE | | bowtie2 | GNU GPLv3 | https://github.com/BenLangmead/bowtie2/blob/master/LICENSE | +| Bracken | GNU GPLv3 | https://github.com/jenniferlu717/Bracken/blob/master/LICENSE | | BUSCO | MIT | https://gitlab.com/ezlab/busco/-/raw/master/LICENSE | | BWA | GNU GPLv3 | https://github.com/lh3/bwa/blob/master/COPYING | | Canu
Racon
Minimap2 | GNU GPLv3 (Canu),
MIT (Racon),
MIT (Minimap2) | https://github.com/marbl/canu/blob/master/README.license.GPL https://github.com/isovic/racon/blob/master/LICENSE https://github.com/lh3/minimap2/blob/master/LICENSE.txt | diff --git a/README.md b/README.md index a64c99cc2..1dabb1a47 100644 --- a/README.md +++ b/README.md @@ -119,6 +119,7 @@ To learn more about the docker pull rate limits and the open source software pro | [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/ | | [bowtie2](https://hub.docker.com/r/staphb/bowtie2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
https://github.com/BenLangmead/bowtie2 | +| [Bracken](https://hub.docker.com/r/staphb/bracken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
https://github.com/jenniferlu717/Bracken | | [BUSCO](https://hub.docker.com/r/staphb/busco/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | | https://busco.ezlab.org/busco_userguide.html
https://gitlab.com/ezlab/busco | | [BWA](https://hub.docker.com/r/staphb/bwa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | | https://github.com/lh3/bwa | | [Canu](https://hub.docker.com/r/staphb/canu)
[![docker pulls](https://badgen.net/docker/pulls/staphb/canu?)](https://hub.docker.com/r/staphb/canu)| | https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu | diff --git a/bracken/2.9/Dockerfile b/bracken/2.9/Dockerfile new file mode 100644 index 000000000..5d335e4c9 --- /dev/null +++ b/bracken/2.9/Dockerfile @@ -0,0 +1,67 @@ +ARG KRAKEN_VER="2.1.3" +ARG BRACKEN_VER="2.9" + +## Builder ## +FROM ubuntu:jammy as builder + +ARG KRAKEN_VER +ARG BRACKEN_VER + +RUN apt-get update && apt-get install -y build-essential perl wget zlib1g-dev + +# 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-${BRACKEN_VER} &&\ + chmod 755 install_bracken.sh && ./install_bracken.sh + +## App ## +FROM ubuntu:jammy as app + +ARG BRACKEN_VER + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="Bracken" +LABEL software.version=${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="kutluhan.incekara@ct.gov" + +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 + +COPY --from=builder /kraken2 /kraken2 +COPY --from=builder /Bracken-${BRACKEN_VER} /Bracken + +ENV LC_ALL=C +ENV PATH="${PATH}:/kraken2:/Bracken" + +CMD [ "bracken", "-h" ] + +WORKDIR /data + +## Test ## +FROM app as test + +RUN apt-get update && apt-get install --no-install-recommends -y wget + +# 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 + +# 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 + +# 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 diff --git a/bracken/2.9/README.md b/bracken/2.9/README.md new file mode 100644 index 000000000..dd1c38fa9 --- /dev/null +++ b/bracken/2.9/README.md @@ -0,0 +1,29 @@ +# Bracken container + +Main tool: [Bracken](https://github.com/jenniferlu717/Bracken) + +Code repository: https://github.com/jenniferlu717/Bracken + +Additional tools: +- kraken2: 2.1.3 +- python: 3.10.12 +- perl: 5.34.0 +- pigz: 2.6 + +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). + +Additional information: + +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. + +Full documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual + +## Example Usage + +```bash +bracken -d database_folder -i kraken_report -o bracken_report -r 75 -l S -t 10 +``` \ No newline at end of file