diff --git a/Program_Licenses.md b/Program_Licenses.md index a3d94a8a1..075159da6 100644 --- a/Program_Licenses.md +++ b/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` | diff --git a/README.md b/README.md index 6977eded9..99e828f9a 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | | [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | | [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | | https://github.com/DerrickWood/kraken | -| [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | +| [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | +| [KrakenTools](https://github.com/jenniferlu717/KrakenTools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/krakentools)](https://hub.docker.com/r/staphb/krakentools) | | https://github.com/jenniferlu717/KrakenTools | | [KrakenUniq](https://hub.docker.com/r/staphb/krakenuniq/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/krakenuniq)](https://hub.docker.com/r/staphb/krakenuniq) | | https://github.com/fbreitwieser/krakenuniq | | [kSNP3](https://hub.docker.com/r/staphb/ksnp3/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ksnp3)](https://hub.docker.com/r/staphb/ksnp3)| | https://sourceforge.net/projects/ksnp/ | | [kSNP4](https://hub.docker.com/r/staphb/ksnp4/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ksnp4)](https://hub.docker.com/r/staphb/ksnp4)| | https://sourceforge.net/projects/ksnp/ | diff --git a/krakentools/d4a2fbe/Dockerfile b/krakentools/d4a2fbe/Dockerfile new file mode 100644 index 000000000..20691e85e --- /dev/null +++ b/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="sagemwright@gmail.com" + + +# 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 \ No newline at end of file diff --git a/krakentools/d4a2fbe/README.md b/krakentools/d4a2fbe/README.md new file mode 100644 index 000000000..8794ae695 --- /dev/null +++ b/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 +```