From 089e54e0594cdd3b8f6397cbd850ae7f409a83ef Mon Sep 17 00:00:00 2001 From: Kincekara Date: Wed, 16 Oct 2024 19:47:02 +0000 Subject: [PATCH] adds checkm2 --- Program_Licenses.md | 1 + README.md | 1 + checkm2/1.0.2/Dockerfile | 37 +++++++++++++++++++++++++++++++++++++ checkm2/1.0.2/README.md | 28 ++++++++++++++++++++++++++++ 4 files changed, 67 insertions(+) create mode 100644 checkm2/1.0.2/Dockerfile create mode 100644 checkm2/1.0.2/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index a3d94a8a1..46d7bbe28 100644 --- a/Program_Licenses.md +++ b/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/ | diff --git a/README.md b/README.md index 6977eded9..274b351ab 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/cdc-spn)](https://hub.docker.com/r/staphb/cdc-spn) | | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference | | [cfsan-snp-pipeline](https://hub.docker.com/r/staphb/cfsan-snp-pipeline)
[![docker pulls](https://badgen.net/docker/pulls/staphb/cfsan-snp-pipeline)](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) | | https://github.com/CFSAN-Biostatistics/snp-pipeline | | [CheckM](https://hub.docker.com/r/staphb/checkm)
[![docker pulls](https://badgen.net/docker/pulls/staphb/checkm)](https://hub.docker.com/r/staphb/checkm) | | https://github.com/Ecogenomics/CheckM | +| [CheckM2](https://hub.docker.com/r/staphb/checkm2)
[![docker pulls](https://badgen.net/docker/pulls/staphb/checkm2)](https://hub.docker.com/r/staphb/checkm2) | | https://github.com/chklovski/CheckM2 | | [CheckV](https://hub.docker.com/r/staphb/checkv)
[![docker pulls](https://badgen.net/docker/pulls/staphb/checkv)](https://hub.docker.com/r/staphb/checkv) | | https://bitbucket.org/berkeleylab/checkv/ | | [Circlator](https://hub.docker.com/r/staphb/circlator)
[![docker pulls](https://badgen.net/docker/pulls/staphb/circlator)](https://hub.docker.com/r/staphb/circlator) | | https://github.com/sanger-pathogens/circlator | | [Circos](https://hub.docker.com/r/staphb/circos)
[![docker pulls](https://badgen.net/docker/pulls/staphb/circos)](https://hub.docker.com/r/staphb/circos) | | https://circos.ca/ | diff --git a/checkm2/1.0.2/Dockerfile b/checkm2/1.0.2/Dockerfile new file mode 100644 index 000000000..ad5f42502 --- /dev/null +++ b/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="${CHECKM2_VERSION}" +LABEL description="Rapid assessment of genome bin quality using machine learning." +LABEL website="https://github.com/chklovski/CheckM2" +LABEL license="https://github.com/chklovski/CheckM2/blob/main/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install -y --no-install-recommends \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN micromamba install --name base -c conda-forge -c bioconda checkm2=${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 \ No newline at end of file diff --git a/checkm2/1.0.2/README.md b/checkm2/1.0.2/README.md new file mode 100644 index 000000000..af4756b7c --- /dev/null +++ b/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 +``` \ No newline at end of file