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* adding ppanggolin * changed to mamba and added tests * added usage
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| ARG PPANGGOLIN_VER="1.2.105" | ||
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| FROM mambaorg/micromamba:1.4.9 as app | ||
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| ARG PPANGGOLIN_VER | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="mambaorg/micromamba:1.4.9" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="PPanGGOLiN" | ||
| LABEL software.version="${PPANGGOLIN_VER}" | ||
| LABEL description="Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors" | ||
| LABEL website="https://github.com/labgem/PPanGGOLiN" | ||
| LABEL license="https://github.com/labgem/PPanGGOLiN/blob/master/LICENSE.txt" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| USER root | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| procps \ | ||
| wget && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| ENV PATH="/opt/conda/envs/base/bin/:/opt/conda/bin/:$PATH" LC_ALL=C | ||
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| RUN micromamba install --name base -c conda-forge -c bioconda -c defaults ppanggolin=${PPANGGOLIN_VER} && \ | ||
| micromamba clean -a -y && \ | ||
| ppanggolin -h && \ | ||
| mkdir /data | ||
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| # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' | ||
| CMD ppanggolin -h | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| FROM app as test | ||
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| ARG PPANGGOLIN_VER | ||
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| WORKDIR /test | ||
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| RUN ppanggolin --help && \ | ||
| ppanggolin --version | ||
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| # getting test files from github repo | ||
| RUN wget -q https://github.com/labgem/PPanGGOLiN/archive/refs/tags/${PPANGGOLIN_VER}.tar.gz && \ | ||
| tar -xvf ${PPANGGOLIN_VER}.tar.gz | ||
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| RUN cd PPanGGOLiN-${PPANGGOLIN_VER}/testingDataset && \ | ||
| ppanggolin annotate --fasta organisms.fasta.list --output output && cp output/pangenome.h5 output/pangenome.1.h5 && \ | ||
| ppanggolin cluster -p output/pangenome.h5 && cp output/pangenome.h5 output/pangenome.2.h5 && \ | ||
| ppanggolin graph -p output/pangenome.h5 && cp output/pangenome.h5 output/pangenome.3.h5 && \ | ||
| ppanggolin partition -p output/pangenome.h5 && cp output/pangenome.h5 output/pangenome.4.h5 && \ | ||
| ppanggolin draw -p output/pangenome.h5 --ucurve && \ | ||
| ppanggolin write -p output/pangenome.h5 --stats --output output_stats && \ | ||
| md5sum output/pangenome*.h5 && \ | ||
| head output_stats/* | ||
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| # PPanGGOLiN container | ||
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| Main tool: [PPanGGOLiN](https://github.com/labgem/PPanGGOLiN) | ||
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| Code repository: https://github.com/labgem/PPanGGOLiN | ||
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| Basic information on how to use this tool: | ||
| - executable: ppanggolin | ||
| - help: --help | ||
| - version: --version | ||
| - description: | | ||
| > PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes. | ||
| Additional information: | ||
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| PPanGGOLiN only creates the pangenome graphs. It is recommended to use another tool to visualize them. Please read https://github.com/labgem/PPanGGOLiN/wiki for more information. | ||
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| Full documentation: https://github.com/labgem/PPanGGOLiN/wiki | ||
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| ## Example Usage | ||
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| ```bash | ||
| ppanggolin annotate --fasta organisms.fasta.list --output output | ||
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| # many of the commands manipulate the 'pangenome.h5' file in place | ||
| ppanggolin cluster -p pangenome.h5 | ||
| ppanggolin graph -p pangenome.h5 | ||
| ppanggolin partition -p pangenome.h5 | ||
| ppanggolin draw -p pangenome.h5 --ucurve | ||
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| # there are some human-readable files that can be generated as well | ||
| ppanggolin write -p pangenome.h5 --stats --output stats | ||
| ``` |