Merge pull request #1078 from Kincekara/checkv

adds checkv

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 |
+| 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/ |
 | CirculoCov | GNU GPLv3 | https://github.com/erinyoung/CirculoCov/blob/main/LICENSE |

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 |
+| [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/ |
 | [CirculoCov](https://hub.docker.com/r/staphb/circulocov) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/circulocov)](https://hub.docker.com/r/staphb/circulocov) | <ul><li>[0.1.20240104](./circulocov/0.1.20240104/)</li></ul> | https://github.com/erinyoung/CirculoCov |

checkv/1.0.3/Dockerfile

@@ -0,0 +1,52 @@
+FROM ubuntu:jammy AS app
+
+ARG CHECKV_VER="1.0.3"
+ARG DIAMOND_VER="2.1.8"
+ARG PRODIGALGV_VER="2.11.0"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="CheckV"
+LABEL software.version="${CHECKV_VER}"
+LABEL description="CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes"
+LABEL website="https://bitbucket.org/berkeleylab/checkv/"
+LABEL license="https://bitbucket.org/berkeleylab/checkv/src/master/LICENSE.txt"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    hmmer \
+    ncbi-blast+ \
+    python3-pip && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install diamond
+RUN wget -q https://github.com/bbuchfink/diamond/releases/download/v${DIAMOND_VER}/diamond-linux64.tar.gz &&\
+    tar -C /usr/local/bin/ -xvf diamond-linux64.tar.gz &&\
+    rm diamond-linux64.tar.gz
+# install prodigal-gv
+RUN wget -q https://github.com/apcamargo/prodigal-gv/releases/download/${PRODIGALGV_VER}/prodigal-gv-linux &&\
+    chmod +x prodigal-gv-linux &&\
+    mv prodigal-gv-linux /usr/local/bin/prodigal-gv
+# install checkv
+RUN pip3 install --no-cache-dir checkv==${CHECKV_VER}
+
+ENV LC_ALL=C
+
+CMD [ "checkv", "--help" ]
+
+WORKDIR /data
+
+
+## Test ##
+FROM app AS test 
+
+# download database (current v1.5)
+RUN checkv download_database /db 
+
+# download test fna and run checkv
+RUN wget -q https://bitbucket.org/berkeleylab/checkv/raw/51a5293f75da04c5d9a938c9af9e2b879fa47bd8/test/test_sequences.fna &&\
+    checkv end_to_end -d /db/checkv-db-v1.5 test_sequences.fna test_out -t 4
+
+

checkv/1.0.3/README.md

@@ -0,0 +1,38 @@
+# CheckV container
+
+Main tool: [checkv](https://jgi.doe.gov/data-and-tools/software-tools/checkv/)
+
+Code repository: https://bitbucket.org/berkeleylab/checkv/
+
+Additional tools:
+- diamond: 2.1.8
+- prodigal-gv: 2.11.0
+- hmmer: 3.3.2
+- blast: 2.12.0+
+
+Basic information on how to use this tool:
+- executable: checkv
+- help: -h
+- version:
+- description: 
+>CheckV is the first fully automated, command-line tool for assessing the quality of metagenome-assembled viral genomes
+
+Additional information:
+
+This container does not include any database. You can use `checkv download_database` command or https://portal.nersc.gov/CheckV/ address to download it manually
+
+Full documentation: https://bitbucket.org/berkeleylab/checkv/src/master/
+
+## Example Usage
+
+```bash
+# Using a single command to run the full pipeline (recommended)
+checkv end_to_end input_file.fna output_directory -t 16
+
+# Using individual commands for each step in the pipeline
+checkv contamination input_file.fna output_directory -t 16
+checkv completeness input_file.fna output_directory -t 16
+checkv complete_genomes input_file.fna output_directory
+checkv quality_summary input_file.fna output_directory
+```
+