adding krona 2.8.1 with krakentools

Program_Licenses.md

@@ -95,6 +95,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Kraken2 | MIT | https://github.com/DerrickWood/kraken2/blob/master/LICENSE |
 | KrakenTools | GNU GPLv3 | https://github.com/jenniferlu717/KrakenTools/blob/master/LICENSE |
 | KrakenUniq | GNU GPLv3 | https://github.com/fbreitwieser/krakenuniq/blob/master/LICENSE |
+| Krona | non-standard license (see link) | https://github.com/marbl/Krona/blob/master/KronaTools/LICENSE.txt |
 | kSNP3 | BSD | available in zipped kSNP archive on sourceforge or in docker image under `/kSNP3.1_Linux_package/THE BSD OPENSOURCE LICENSE.pdf` |
 | kSNP4 | BSD | available in zipped kSNP archive on sourceforge or in docker image under `/opt/kSNP4 Linux package/Documentation/THE BSD OPENSOURCE LICENSE.pdf` |
 | LABEL | GPL version 3 | In zipped file in README.md |

README.md

@@ -205,6 +205,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Kraken2](https://hub.docker.com/r/staphb/kraken2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | <ul><li>2.0.8-beta (no database)</li><li>2.0.8-beta (MiniKraken2_v1_8GB db)</li><li>2.0.8-beta_hv (human + virus db)</li><li>2.0.9-beta (no db)</li><li>2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)</li><li>2.1.0 (no db)</li><li>2.1.1 (no db)</li><li>2.1.2 (no db)</li><li>[2.1.3](kraken2/2.1.3/) (no db)</li></ul> | https://github.com/DerrickWood/kraken2 | 
 | [KrakenTools](https://github.com/jenniferlu717/KrakenTools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/krakentools)](https://hub.docker.com/r/staphb/krakentools) | <ul><li>[d4a2fbe](./krakentools/d4a2fbe)</li></ul> | https://github.com/jenniferlu717/KrakenTools |
 | [KrakenUniq](https://hub.docker.com/r/staphb/krakenuniq/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/krakenuniq)](https://hub.docker.com/r/staphb/krakenuniq) | <ul><li>[1.0.4](./krakenuniq/1.0.4) (no database)</li></ul> | https://github.com/fbreitwieser/krakenuniq |
+| [Krona](https://hub.docker.com/r/staphb/krona/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/krona)](https://hub.docker.com/r/staphb/krona) | <ul><li>[2.8.1](./krona/2.8.1)</li></ul> | https://github.com/marbl/Krona |
 | [kSNP3](https://hub.docker.com/r/staphb/ksnp3/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ksnp3)](https://hub.docker.com/r/staphb/ksnp3)| <ul><li>3.1</li></ul> | https://sourceforge.net/projects/ksnp/ |
 | [kSNP4](https://hub.docker.com/r/staphb/ksnp4/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ksnp4)](https://hub.docker.com/r/staphb/ksnp4)| <ul><li>4.0</li><li>[4.1](./ksnp4/4.1/)</li></ul> | https://sourceforge.net/projects/ksnp/ |
 | [label](https://hub.docker.com/r/staphb/label/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/label)](https://hub.docker.com/r/staphb/label)| <ul><li>[0.6.4](./label/0.6.4/)</li></ul> | https://wonder.cdc.gov/amd/flu/label |

build-files/krona/Dockerfile

@@ -0,0 +1,55 @@
+FROM ubuntu:jammy AS app
+
+ARG KRONA_VER="2.8.1"
+ARG KRAKENTOOLS_VER="d4a2fbe"
+
+LABEL base_image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="krona"
+LABEL software.version="${KRONA_VER}"
+LABEL description="Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files."
+LABEL website="https://github.com/marbl/Krona"
+LABEL license="https://github.com/marbl/Krona/blob/master/KronaTools/LICENSE.txt"
+LABEL maintainer="Sage Wright"
+LABEL maintainer.email="[email protected]"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    curl \
+    python3 \
+    python3-pip \
+    python3-setuptools \
+    git \
+    make \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p ~/miniconda3 && \
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh && \
+    bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 && \
+    rm ~/miniconda3/miniconda.sh
+
+ENV PATH="/root/miniconda3/bin:$PATH"
+
+RUN conda install -c bioconda krona=${KRONA_VER} && \
+    ktUpdateTaxonomy.sh
+
+RUN pip install biopython==1.84 \
+    pandas==2.2.3
+
+RUN git clone https://github.com/jenniferlu717/KrakenTools.git && \
+    cd KrakenTools && \
+    git checkout ${KRAKENTOOLS_VERSION} && \
+    chmod +x *
+
+ENV PATH=/KrakenTools:${PATH}
+
+WORKDIR /data
+
+FROM app AS test
+
+RUN python3 /KrakenTools/extract_kraken_reads.py --help
+RUN ktImportTaxonomy
+

build-files/krona/README.md

@@ -0,0 +1,35 @@
+
+# Krona container
+
+Main tool: [Krona](https://github.com/marbl/Krona)
+
+Code repository: <https://github.com/marbl/Krona/tree/master/KronaTools>
+
+Additional tools:
+
+- krona 2.8.1
+- krakentools d4a2fbe
+- pandas 2.2.3
+- bioptyhon 1.84
+- miniconda (latest)
+
+Basic information on how to use this tool:
+- executable: various perl scripts
+- help: provide the tool name without any arguments to see the help message (`<toolname>`)
+- version: Versioning information is available within the help message and can be retrieved with the following grep command `<toolname> | grep "KronaTools" | cut -d' ' -f3`
+- description: "Krona allows hierarchical data to be explored with zooming, multi-layered pie charts... The interactive charts are self-contained and can be viewed with any modern web browser."
+
+Additional information: This container also contains [KrakenTools](https://github.com/jenniferlu717/KrakenTools), which provides a way for Krona plots to be generated for viral data.
+
+Full documentation: [https://github.com/marbl/Krona](https://github.com/marbl/Krona/wiki)
+
+## Example Usage
+
+```bash
+# run Krona without preprocessing of the kraken output by Krakentools -- viral data will be considered "other root" but bacterial data will be visualized
+ktImportTaxonomy MYSAMPLE.kraken_output_report -o MYSAMPLE.krona.hmtl -tax taxonomy
+
+# run Krona with preprocessing of the kraken output by Krakentools in order to visualize viral data properly
+python3 /KrakenTools/kreport2krona.py -r MYSAMPLE.kraken_output_report -o MYSAMPLE.krona 
+ktImportText MYSAMPLE.krona -o MYSAMPLE.krona.html
+```