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Merge pull request #811 from Kincekara/aniclustermap
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add ANIclustermap
erinyoung authored Dec 4, 2023

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1 change: 1 addition & 0 deletions Program_Licenses.md
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| Software | License | Link to license |
| :--------: | :-------: | -------- |
| ABRicate | GNU GPLv2 | https://github.com/tseemann/abricate/blob/master/LICENSE |
| ANIclustermap | MIT | https://github.com/moshi4/ANIclustermap/blob/main/LICENSE |
| artic | MIT | https://github.com/artic-network/fieldbioinformatics/blob/master/LICENSE |
| artic-ncov2019-epi2me | MPL 2.0 | https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE |
| any2fasta | GNU GPLv3 | https://github.com/tseemann/any2fasta/blob/master/LICENSE |
1 change: 1 addition & 0 deletions README.md
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| Software | Version | Link |
| :--------: | ------- | -------- |
| [ABRicate](https://hub.docker.com/r/staphb/abricate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/abricate)](https://hub.docker.com/r/staphb/abricate) | <ul><li>0.8.7</li><li>0.8.13</li><li>0.8.13s (+serotypefinder db)</li><li>0.9.8</li><li>1.0.0</li><li>[1.0.1 (+ A. baumannii plasmid typing db)](https://github.com/StaPH-B/docker-builds/blob/master/abricate/1.0.1-Abaum-plasmid)</li><li>[1.0.1 (+ InsaFlu db)](https://github.com/StaPH-B/docker-builds/blob/master/abricate/1.0.1-insaflu-220727)</li></ul> | https://github.com/tseemann/abricate |
| [ANIclustermap](https://hub.docker.com/r/staphb/aniclustermap/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/aniclustermap)](https://hub.docker.com/r/staphb/aniclustermap) | <ul><li>[1.3.0](aniclusteramp/1.3.0/)</li></ul> | https://github.com/moshi4/ANIclustermap |
| [any2fasta](https://hub.docker.com/r/staphb/any2fasta/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/any2fasta)](https://hub.docker.com/r/staphb/any2fasta) | <ul><li>0.4.2</li></ul> | https://github.com/tseemann/any2fasta |
| [ARIBA](https://hub.docker.com/r/staphb/ariba/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ariba)](https://hub.docker.com/r/staphb/ariba) | <ul><li>2.14.4</li><li>[2.14.6](ariba/2.14.6/)</li></ul> | https://github.com/sanger-pathogens/ariba |
| [artic](https://hub.docker.com/r/staphb/artic-ncov2019) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic)](https://hub.docker.com/r/staphb/artic) | <ul><li>[1.2.4-1.11.1 (artic-medaka)](artic/1.2.4-1.11.1/)</ul> | https://github.com/artic-network/fieldbioinformatics |
61 changes: 61 additions & 0 deletions aniclustermap/1.3.0/Dockerfile
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ARG ANICLUSTERMAP_VER="1.3.0"
ARG FASTANI_VER="1.34"
ARG SKANI_VER="0.2.1"

FROM staphb/fastani:${FASTANI_VER} as fastani
FROM staphb/skani:${SKANI_VER} as skani

## App ##
FROM ubuntu:jammy as app

ARG ANICLUSTERMAP_VER

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]"

# 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}

# import fastani & skani
COPY --from=fastani /usr/local/bin/fastANI /usr/local/bin/
COPY --from=skani /usr/local/bin/skani /usr/local/bin/

# default run command
CMD ANIclustermap -h

# singularity compatibility
ENV LC_ALL=C

WORKDIR /data

## Test ##
FROM app as test

ARG ANICLUSTERMAP_VER

RUN apt-get update && apt-get install -y wget

# 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

24 changes: 24 additions & 0 deletions aniclustermap/1.3.0/README.md
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# ANIclustermap container

Main tool: [ANIclustermap](https://github.com/moshi4/ANIclustermap)

Code repository: https://github.com/moshi4/ANIclustermap

Additional tools:
- fastANI: 1.34
- skani: 0.2.1

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.


Full documentation: https://github.com/moshi4/ANIclustermap

## Example Usage

```bash
ANIclustermap -i input_directory -o output_directory
```

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