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Merge pull request #811 from Kincekara/aniclustermap
add ANIclustermap
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ARG ANICLUSTERMAP_VER="1.3.0" | ||
ARG FASTANI_VER="1.34" | ||
ARG SKANI_VER="0.2.1" | ||
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FROM staphb/fastani:${FASTANI_VER} as fastani | ||
FROM staphb/skani:${SKANI_VER} as skani | ||
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## App ## | ||
FROM ubuntu:jammy as app | ||
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ARG ANICLUSTERMAP_VER | ||
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LABEL base.image="ubuntu:jammy" | ||
LABEL dockerfile.version="1" | ||
LABEL software="ANIclustermap" | ||
LABEL software.version="${ANICLUSTERMAP_VER}" | ||
LABEL description="ANIclustermap draws ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes." | ||
LABEL website="https://github.com/moshi4/ANIclustermap" | ||
LABEL license="https://github.com/moshi4/ANIclustermap/blob/main/LICENSE" | ||
LABEL maintainer="Kutluhan Incekara" | ||
LABEL maintainer.email="[email protected]" | ||
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# install aniclustermap and its dependencies | ||
RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
python3-pip \ | ||
libgomp1 &&\ | ||
apt-get autoclean && rm -rf /var/lib/apt/lists/* &&\ | ||
pip install aniclustermap==${ANICLUSTERMAP_VER} | ||
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# import fastani & skani | ||
COPY --from=fastani /usr/local/bin/fastANI /usr/local/bin/ | ||
COPY --from=skani /usr/local/bin/skani /usr/local/bin/ | ||
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# default run command | ||
CMD ANIclustermap -h | ||
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# singularity compatibility | ||
ENV LC_ALL=C | ||
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WORKDIR /data | ||
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## Test ## | ||
FROM app as test | ||
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ARG ANICLUSTERMAP_VER | ||
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RUN apt-get update && apt-get install -y wget | ||
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# download test data from repo | ||
RUN wget https://github.com/moshi4/ANIclustermap/archive/refs/tags/v${ANICLUSTERMAP_VER}.tar.gz &&\ | ||
tar -xvf v${ANICLUSTERMAP_VER}.tar.gz | ||
# run default fastani mode | ||
RUN ANIclustermap -i ANIclustermap-${ANICLUSTERMAP_VER}/example/input/minimal_dataset/ -o fastani | ||
# run skani mode | ||
RUN ANIclustermap -m skani -i ANIclustermap-${ANICLUSTERMAP_VER}/example/input/minimal_dataset/ -o skani | ||
# check results | ||
RUN ls fastani &&\ | ||
cat fastani/ANIclustermap_matrix.tsv &&\ | ||
ls skani &&\ | ||
cat skani/ANIclustermap_matrix.tsv | ||
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# ANIclustermap container | ||
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Main tool: [ANIclustermap](https://github.com/moshi4/ANIclustermap) | ||
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Code repository: https://github.com/moshi4/ANIclustermap | ||
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Additional tools: | ||
- fastANI: 1.34 | ||
- skani: 0.2.1 | ||
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Basic information on how to use this tool: | ||
- executable: ANIclustermap | ||
- help: -h, --help | ||
- version: -v, --version | ||
- description: ANIclustermap is easy-to-use tool for drawing ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes. | ||
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Full documentation: https://github.com/moshi4/ANIclustermap | ||
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## Example Usage | ||
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```bash | ||
ANIclustermap -i input_directory -o output_directory | ||
``` |