adding krakentools version d4a2fbe

Program_Licenses.md

@@ -85,6 +85,7 @@ The licenses of the open-source software that is contained in these Docker image
 | kma | Apache v2.0 | https://bitbucket.org/genomicepidemiology/kma/src/master/ |
 | Kraken | GNU GPLv3 | https://github.com/DerrickWood/kraken/blob/master/LICENSE |
 | 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 |
 | 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` |

README.md

@@ -193,7 +193,8 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <ul><li>[2.0.4](./kleborate/2.0.4/)</li><li>[2.1.0](./kleborate/2.1.0/)</li><li>[2.2.0](./kleborate/2.3.2/)</li><li>[2.3.2](./kleborate/2.3.2)</li><li>[2.3.2-2023-05](kleborate/2.3.2-2023-05/)</li><li>[2.4.1](kleborate/2.4.1/)</li></ul> | https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/ |
 | [kma](https://hub.docker.com/r/staphb/kma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | <ul><li>1.2.21</li><li>1.4.10 (no database)</li><li>[1.4.14](./kma/1.4.14/) (no database)</li></ul> | https://bitbucket.org/genomicepidemiology/kma/ |
 | [Kraken](https://hub.docker.com/r/staphb/kraken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | <ul><li>1.0</li><li>1.1.1</li><li>1.1.1 (no database)</li></ul> | https://github.com/DerrickWood/kraken |
-| [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 |
+| [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 |
 | [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/ |

krakentools/d4a2fbe/Dockerfile

@@ -0,0 +1,47 @@
+FROM ubuntu:jammy AS app
+
+WORKDIR /
+
+# using a git commit because the last release was over three years ago, despite recent(ish) activity in the repo's main branch
+# this commit is from 2023-11-16: https://github.com/jenniferlu717/KrakenTools/commit/d4a2fbe2833c2392a724697c0c97a3014e748474
+ARG KRAKENTOOLS_VERSION="d4a2fbe2833c2392a724697c0c97a3014e748474"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="KrakenTools"
+LABEL software.version=${KRAKENTOOLS_VERSION}
+LABEL description="KrakenTools is a set of tools for processing Kraken output"
+LABEL website="https://github.com/jenniferlu717/KrakenTools"
+LABEL documentation="https://github.com/jenniferlu717/KrakenTools"
+LABEL license="https://github.com/jenniferlu717/KrakenTools/blob/master/LICENSE"
+LABEL maintainer="Sage Wright"
+LABEL maintainer.email="[email protected]"
+
+
+# Install dependencies via apt-get; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    python3 \
+    python3-pip \
+    python3-setuptools \
+    git \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+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

krakentools/d4a2fbe/README.md

@@ -0,0 +1,29 @@
+# KrakenTools container
+
+Main tool [KrakenTools](https://github.com/jenniferlu717/KrakenTools)
+
+Code repository: https://github.com/jenniferlu717/KrakenTools
+
+Additional tools:
+
+- python 3.10.12
+- biopython 1.84
+- pandas 2.2.3
+- numpy 2.1.2
+
+Basic information on how to use this tool:
+
+- executable: various python scripts
+- help: most scripts have -h options
+- version: most scripts do not have versioning information
+- description: "KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results."
+
+Additional information:
+
+Full documentation: [https://github.com/jenniferlu717/KrakenTools](https://github.com/jenniferlu717/KrakenTools)
+
+## Example Usage
+
+```bash
+python3 /KrakenTools/extract_kraken_reads.py -h
+```