Merge pull request #1080 from Kincekara/checkm2

adds checkm2

Program_Licenses.md

@@ -31,6 +31,7 @@ The licenses of the open-source software that is contained in these Docker image
 | CDC-SPN | GitHub No License | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
 | cfsan-snp-pipeline | non-standard license see --> | https://github.com/CFSAN-Biostatistics/snp-pipeline/blob/master/LICENSE.txt |
 | CheckM | GNU GPLv3 | https://github.com/Ecogenomics/CheckM/blob/master/LICENSE |
+| CheckM2 | GNU GPLv3 | https://github.com/chklovski/CheckM2/blob/main/LICENSE |
 | CheckV | MIT | https://bitbucket.org/berkeleylab/checkv/src/master/LICENSE.txt |
 | Circlator | GNU GPLv3 | https://github.com/sanger-pathogens/circlator/blob/master/LICENSE |
 | Circos | GNU GPLv3 | https://circos.ca/ |

README.md

@@ -139,6 +139,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [CDC-SPN](https://hub.docker.com/r/staphb/cdc-spn/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cdc-spn)](https://hub.docker.com/r/staphb/cdc-spn) | <ul><li>0.1 (no version)</li></ul> | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
 | [cfsan-snp-pipeline](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cfsan-snp-pipeline)](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) | <ul><li>2.0.2</li> <li>2.2.1</li> </ul> | https://github.com/CFSAN-Biostatistics/snp-pipeline |
 | [CheckM](https://hub.docker.com/r/staphb/checkm) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/checkm)](https://hub.docker.com/r/staphb/checkm) | <ul><li>[1.2.2](./checkm/1.2.2/)</li><li>[1.2.3](./checkm/1.2.3/)</li></ul> | https://github.com/Ecogenomics/CheckM |
+| [CheckM2](https://hub.docker.com/r/staphb/checkm2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/checkm2)](https://hub.docker.com/r/staphb/checkm2) | <ul><li>[1.0.2](./checkm2/1.0.2)</li></ul> | https://github.com/chklovski/CheckM2 |
 | [CheckV](https://hub.docker.com/r/staphb/checkv) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/checkv)](https://hub.docker.com/r/staphb/checkv) | <ul><li>[1.0.3](./checkv/1.0.3/)</li></ul> | https://bitbucket.org/berkeleylab/checkv/ |
 | [Circlator](https://hub.docker.com/r/staphb/circlator) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/circlator)](https://hub.docker.com/r/staphb/circlator) | <ul><li>1.5.6</li><li>1.5.5</li></ul> | https://github.com/sanger-pathogens/circlator |
 | [Circos](https://hub.docker.com/r/staphb/circos) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/circos)](https://hub.docker.com/r/staphb/circos) | <ul><li>[0.69-9](./circos/0.69.9/)</li></ul> | https://circos.ca/ |

checkm2/1.0.2/Dockerfile

@@ -0,0 +1,37 @@
+FROM mambaorg/micromamba:1.5.8 AS app
+
+ARG CHECKM2_VERSION="1.0.2"
+
+USER root
+
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="CHECKM2"
+LABEL software.version="${CHECKM2_VERSION}"
+LABEL description="Rapid assessment of genome bin quality using machine learning."
+LABEL website="https://github.com/chklovski/CheckM2"
+LABEL license="https://github.com/chklovski/CheckM2/blob/main/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda checkm2=${CHECKM2_VERSION} && \
+    micromamba clean -a -f -y
+
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+CMD [ "checkm2", "--help" ]
+
+WORKDIR /data
+
+## Test ##
+FROM app AS test 
+
+RUN checkm2 database --download &&\
+    checkm2 testrun --threads 4

checkm2/1.0.2/README.md

@@ -0,0 +1,28 @@
+# CheckM2 container
+
+Main tool: [checkm2](https://github.com/chklovski/CheckM2)
+
+Code repository: https://github.com/chklovski/CheckM2
+
+Additional tools:
+- diamond: 2.0.4
+- prodigal 2.6.3
+
+Basic information on how to use this tool:
+- executable: checkm2
+- help: -h, --help
+- version: --version
+- description: Rapid assessment of genome bin quality using machine learning.
+
+Additional information:
+
+CheckM2 relies on a external diamond database (~1.7 GB) for rapid annotation. the database can be downloaded via `checkm2 database --download` command or obtained directly from: https://zenodo.org/api/records/5571251/files/checkm2_database.tar.gz/content
+
+
+Full documentation: https://github.com/chklovski/CheckM2
+
+## Example Usage
+
+```bash
+checkm2 predict --threads 8 fasta --input ./input_folder --output-directory ./output_folder --database_path /path/to/database/CheckM2_database/uniref100.KO.1.dmnd
+```