add ANIclustermap

Program_Licenses.md

@@ -7,6 +7,7 @@ The licenses of the open-source software that is contained in these Docker image
 | 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 |

README.md

@@ -105,6 +105,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | 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 |

aniclustermap/1.3.0/Dockerfile

@@ -0,0 +1,61 @@
+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
+

aniclustermap/1.3.0/README.md

@@ -0,0 +1,24 @@
+# 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
+```