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* Add ppanggolin version 2.0.2 * Update to 2.0.3 * Update to 2.0.3 * Update to 2.0.3
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ARG PPANGGOLIN_VER="2.0.3" | ||
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FROM mambaorg/micromamba:1.5.6 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:1.5.6" | ||
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 all --fasta genomes.fasta.list --output output |
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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 | ||
``` |