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Merge pull request #887 from Kincekara/gubbins
adds gubbins
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FROM mambaorg/micromamba:1.5.6 as app | ||
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ARG GUBBINS_VER="3.3.3" | ||
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USER root | ||
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WORKDIR / | ||
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LABEL base.image="mambaorg/micromamba:1.5.6" | ||
LABEL dockerfile.version="1" | ||
LABEL software="Gubbins" | ||
LABEL software.version="${GUBBINS_VER}" | ||
LABEL description="Genealogies Unbiased By recomBinations In Nucleotide Sequences" | ||
LABEL website="https://github.com/nickjcroucher/gubbins" | ||
LABEL license="https://github.com/nickjcroucher/gubbins/blob/master/LICENSE" | ||
LABEL maintainer="Kutluhan Incekara" | ||
LABEL maintainer.email="[email protected]" | ||
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RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
procps &&\ | ||
apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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RUN micromamba install --name base -c conda-forge -c bioconda gubbins=${GUBBINS_VER} && \ | ||
micromamba clean -a -y && \ | ||
mkdir /data | ||
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ENV PATH="/opt/conda/bin/:${PATH}" \ | ||
LC_ALL=C.UTF-8 | ||
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CMD ["run_gubbins.py", "-h"] | ||
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WORKDIR /data | ||
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FROM app as test | ||
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ENV ENV_NAME="base" | ||
ARG MAMBA_DOCKERFILE_ACTIVATE=1 | ||
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WORKDIR /test | ||
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RUN curl -LJO https://github.com/nickjcroucher/gubbins/raw/master/tests/data/alignment_file_multiple_lines_per_sequence.aln &&\ | ||
run_gubbins.py alignment_file_multiple_lines_per_sequence.aln | ||
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# Gubbins container | ||
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Main tool: [Gubbins](https://github.com/nickjcroucher/gubbins) | ||
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Code repository: https://github.com/nickjcroucher/gubbins | ||
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Additional tools: | ||
- RAxML: 8.2.12 | ||
- FastTree: 2.1.11 | ||
- IQTree: 2.0.3 | ||
- RAxML-NG: 1.0.1 | ||
- Rapidnj: 2.3.2 | ||
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Basic information on how to use this tool: | ||
- executable: run_gubbins.py | ||
- help: -h | ||
- version: --version | ||
- description: Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically divergent from the set of analyzed sequences. | ||
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Full documentation: https://github.com/nickjcroucher/gubbins/blob/master/docs/gubbins_manual.md | ||
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## Example Usage | ||
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```bash | ||
run_gubbins.py fasta_alignment.aln | ||
``` |