recipe mvip

MVP v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes and isolate genomes.

Homepage:

https://gitlab.com/ccoclet/mvp

License:

GNU GENERAL PUBLIC LICENSE

Recipe:

/mvip/meta.yaml

package mvip

versions:

1.1.5-1,  1.1.5-0,  1.1.4-0,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-1,  1.1.0-0,  1.0.0-0

depends bowtie2:

depends checkv:

depends coverm:

depends dos2unix:

depends fasttree:

depends flit:

depends genomad:

1.7.4

depends importlib_resources:

depends mafft:

depends minimap2:

depends mmseqs2:

depends numpy:

1.23

depends pandas:

depends parallel:

depends python:

>=3.7

depends rpy2:

depends samtools:

depends scikit-learn:

0.23

depends seqtk:

depends table2asn:

depends taxopy:

depends tqdm:

depends trimal:

depends vrhyme:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install mvip

and update with::

   mamba update mvip

To create a new environment, run:

mamba create --name myenvname mvip

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/mvip:<tag>

(see `mvip/tags`_ for valid values for ``<tag>``)

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