Merge pull request #773 from Kincekara/checkm

adds checkm

Program_Licenses.md

@@ -24,6 +24,7 @@ The licenses of the open-source software that is contained in these Docker image
 | centroid | GitHub No License | https://github.com/https://github.com/stjacqrm/centroid |
 | 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 |
 | Circlator | GNU GPLv3 | https://github.com/sanger-pathogens/circlator/blob/master/LICENSE |
 | colorid | MIT | https://github.com/hcdenbakker/colorid/blob/master/LICENSE |
 | datasets-sars-cov-2 | Apache 2.0 | https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE |

README.md

@@ -127,6 +127,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [centroid](https://hub.docker.com/r/staphb/centroid/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/centroid)](https://hub.docker.com/r/staphb/centroid) | <ul><li>1.0.0</li></ul> | https://github.com/stjacqrm/centroid |
 | [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></ul> | https://github.com/Ecogenomics/CheckM |
 | [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 |
 | [Clustalo](https://hub.docker.com/r/staphb/clustalo) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/clustalo)](https://hub.docker.com/r/staphb/clustalo) | <ul><li>1.2.4</li></ul> | http://www.clustal.org/omega/ |
 | [colorid](https://hub.docker.com/r/staphb/colorid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/colorid)](https://hub.docker.com/r/staphb/colorid) | <ul><li>0.1.4.3</li></ul> | https://github.com/hcdenbakker/colorid |

checkm/1.2.2/Dockerfile

@@ -0,0 +1,49 @@
+FROM ubuntu:jammy as app
+
+ARG CHECKM_VER="1.2.2"
+ARG PPLACER_VER="v1.1.alpha19"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="CheckM"
+LABEL software.version="${CHECKM_VER}"
+LABEL description="CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes."
+LABEL website="dockerfile-template/Dockerfile dockerfile-template/README.md"
+LABEL license="https://github.com/Ecogenomics/CheckM/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+# install system requirements
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    unzip \
+    python3-pip \
+    hmmer \
+    prodigal &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install checkm and its dependencies
+RUN pip install --no-cache-dir numpy matplotlib pysam checkm-genome &&\
+    wget https://github.com/matsen/pplacer/releases/download/${PPLACER_VER}/pplacer-linux-${PPLACER_VER}.zip && \
+    unzip pplacer-linux-${PPLACER_VER}.zip && rm pplacer-linux-${PPLACER_VER}.zip
+
+ENV PATH=$PATH:/pplacer-Linux-${PPLACER_VER} \
+    LC_ALL=C
+
+# 'CMD' instructions set a default command when the container is run.
+CMD [ "checkm", "-h" ]
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+# download database and inform CheckM of where the files have been placed
+RUN wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz &&\
+    mkdir checkm_db && tar -C checkm_db -xvf checkm_data_2015_01_16.tar.gz &&\
+    checkm data setRoot checkm_db 
+
+# run test with internal test data
+RUN checkm taxonomy_wf species "Escherichia coli" ./checkm_db/test_data/ ./checkm_test_results
+

checkm/1.2.2/README.md

@@ -0,0 +1,36 @@
+# CheckM container
+
+Main tool: [CheckM](https://github.com/Ecogenomics/CheckM)
+
+Code repository: https://github.com/Ecogenomics/CheckM
+
+Additional tools:
+- HHMER: 3.3.2
+- prodigal: 2.6.3
+- pplacer: 1.1.alpha19-0-g807f6f3
+
+Basic information on how to use this tool:
+- executable: checkm
+- help: <-h>
+- version: <-h>
+- description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
+
+Additional information:
+
+This container does not include precalculated data files that CheckM relies on</br>
+Those files can be downloaded from either:
+- https://data.ace.uq.edu.au/public/CheckM_databases
+- https://zenodo.org/record/7401545#.Y44ymHbMJD8
+
+The reference data must be decompress into a directory. Inform CheckM of where the files have been placed with the following command:
+```
+checkm data setRoot <checkm_database_dir>
+```
+
+Full documentation: https://github.com/Ecogenomics/CheckM/wiki
+
+## Example Usage
+
+```bash
+checkm lineage_wf -t 8 -x fasta input_folder output_folder
+```