taavipall/mvp repository overview

foo@bar:~$ docker run \
  --user=${UID}:${GID} \
  -v $(pwd):$(pwd) -w $(pwd) --rm \
  taavipall/mvp:1.1.4
MVP v1.1.4: assessing the quality of metagenome-assembled viral genomes
https://gitlab.com/ccoclet/mvp

usage: mvip <program> [options]

programs:
    MVP_00_set_up_MVP                   Check for any potential errors/issues in the metadata and the sequencing/read files, create all the directories that MVP needs, and install the latest versions of geNomad and checkV databases.
    MVP_01_run_genomad_checkv           Run geNomad and CheckV.
    MVP_02_filter_genomad_checkv        Merge and filter geNomad and CheckV outputs.
    MVP_03_do_clustering                Sequence clustering based on pairwise ANI.
    MVP_04_do_read_mapping              Run CoverM to calculate coverage based on read mapping, using the sorted BAM files sorted by reference, and return to one tabular file per sample.
    MVP_05_create_vOTU_table            Merge all the CoverM output tables and create a set of viral OTU tables based on the cutoffs (i.e., horizontal coverage) and filtration mode (i.e., conservative and relaxed).
    MVP_06_do_functional_annotation     Functional annotation of protein sequences against multiple databases.
    MVP_07_do_binning                   Run vRhyme for binning virus genomes and return outputs.
    MVP_99_prep_MIUViG_submission       Additional module to assist with submitting metagenome-assembled viral genome(s) to GenBank, including MIUViG metadata.
    MVP_100_summarize_outputs           Summarize outputs and create figures.

optional arguments:
  -h, --help  show this help message and exit

FROM mambaorg/micromamba:2.0.2-alpine3.19

COPY --chown=$MAMBA_USER:$MAMBA_USER mvp_environment.yaml /tmp/env.yaml
RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

ARG MAMBA_DOCKERFILE_ACTIVATE=1
COPY pyproject.toml README.md LICENSE VERSION.txt /mvp/
COPY mvip /mvp/mvip/
RUN pip install /mvp

ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "mvip"]