diff --git a/Program_Licenses.md b/Program_Licenses.md index e3ea7d218..f4241b65c 100644 --- a/Program_Licenses.md +++ b/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 | diff --git a/README.md b/README.md index 49450e902..e3db52413 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/abricate)](https://hub.docker.com/r/staphb/abricate) | | https://github.com/tseemann/abricate | +| [ANIclustermap](https://hub.docker.com/r/staphb/aniclustermap/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/aniclustermap)](https://hub.docker.com/r/staphb/aniclustermap) | | https://github.com/moshi4/ANIclustermap | | [any2fasta](https://hub.docker.com/r/staphb/any2fasta/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/any2fasta)](https://hub.docker.com/r/staphb/any2fasta) | | https://github.com/tseemann/any2fasta | | [ARIBA](https://hub.docker.com/r/staphb/ariba/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ariba)](https://hub.docker.com/r/staphb/ariba) | | https://github.com/sanger-pathogens/ariba | | [artic](https://hub.docker.com/r/staphb/artic-ncov2019)
[![docker pulls](https://badgen.net/docker/pulls/staphb/artic)](https://hub.docker.com/r/staphb/artic) | | https://github.com/artic-network/fieldbioinformatics | diff --git a/aniclustermap/1.3.0/Dockerfile b/aniclustermap/1.3.0/Dockerfile new file mode 100644 index 000000000..6b36d79dd --- /dev/null +++ b/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="${ANICLUSTERMAP_VER}" +LABEL description="ANIclustermap draws ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes." +LABEL website="https://github.com/moshi4/ANIclustermap" +LABEL license="https://github.com/moshi4/ANIclustermap/blob/main/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +# install aniclustermap and its dependencies +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3-pip \ + libgomp1 &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* &&\ + pip install aniclustermap==${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 + diff --git a/aniclustermap/1.3.0/README.md b/aniclustermap/1.3.0/README.md new file mode 100644 index 000000000..9a9da72a2 --- /dev/null +++ b/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 +```