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adding krakentools version d4a2fbe (#1079)
* add genoflu * add readme * add to license * add --force-pkgs-dirs * krakentools add * update readmes * silence warnings about AS casing; fix typo * added comment in dockerfile & added additional dependencies and versions to readme for krakentools * pinning biopython and pandas versions and removing unnecessary jq and gawk * fixed version of python installed listed in krakentools readme --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| FROM ubuntu:jammy AS app | ||
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| WORKDIR / | ||
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| # 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" | ||
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| # 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]" | ||
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| # 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/* | ||
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| RUN pip install biopython==1.84 \ | ||
| pandas==2.2.3 | ||
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| RUN git clone https://github.com/jenniferlu717/KrakenTools.git && \ | ||
| cd KrakenTools && \ | ||
| git checkout ${KRAKENTOOLS_VERSION} && \ | ||
| chmod +x * | ||
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| ENV PATH=/KrakenTools:${PATH} | ||
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| WORKDIR /data | ||
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| FROM app AS test | ||
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| RUN python3 /KrakenTools/extract_kraken_reads.py --help |
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| # KrakenTools container | ||
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| Main tool [KrakenTools](https://github.com/jenniferlu717/KrakenTools) | ||
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| Code repository: https://github.com/jenniferlu717/KrakenTools | ||
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| Additional tools: | ||
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| - python 3.10.12 | ||
| - biopython 1.84 | ||
| - pandas 2.2.3 | ||
| - numpy 2.1.2 | ||
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| Basic information on how to use this tool: | ||
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| - 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." | ||
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| Additional information: | ||
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| Full documentation: [https://github.com/jenniferlu717/KrakenTools](https://github.com/jenniferlu717/KrakenTools) | ||
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| ## Example Usage | ||
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| ```bash | ||
| python3 /KrakenTools/extract_kraken_reads.py -h | ||
| ``` |