add bracken

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 <br/> Racon <br/> Minimap2 | GNU GPLv3 (Canu), <br/> MIT (Racon), <br/> 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 |

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/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |
 | [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>2.13.0</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
 | [bowtie2](https://hub.docker.com/r/staphb/bowtie2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | <ul><li>2.4.4</li><li>2.4.5</li><li>2.5.1</li></ul> | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2 |
+| [Bracken](https://hub.docker.com/r/staphb/bracken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | <ul><li>[2.9](./bracken/2.9)</li></ul> | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken |
 | [BUSCO](https://hub.docker.com/r/staphb/busco/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | <ul><li>5.4.7</li></ul> | https://busco.ezlab.org/busco_userguide.html <br/>https://gitlab.com/ezlab/busco |
 | [BWA](https://hub.docker.com/r/staphb/bwa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bwa)](https://hub.docker.com/r/staphb/bwa) | <ul><li>0.7.17</li></ul> | https://github.com/lh3/bwa |
 | [Canu](https://hub.docker.com/r/staphb/canu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/canu?)](https://hub.docker.com/r/staphb/canu)| <ul><li>2.0</li><li>2.1.1</li><li>2.2</li></ul> | https://canu.readthedocs.io/en/latest/ <BR/> https://github.com/marbl/canu |

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="[email protected]"
+
+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

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
+```