recipe checkv

Assess the quality of metagenome-assembled viral genomes.

Homepage:

https://bitbucket.org/berkeleylab/checkv

License:

BSD / Modified BSD

Recipe:

/checkv/meta.yaml

Links:

biotools: checkv, doi: 10.1038/s41587-020-00774-7

package checkv

versions:

1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.9.0-0,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.7.0-1, 

1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.9.0-0,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.7.0-1,  0.7.0-0,  0.6.0-1,  0.6.0-0,  0.5.1-1,  0.5.1-0,  0.4.0-1,  0.4.0-0,  0.3.0-0,  0.2.0-0,  0.1.0-0

depends biopython:

depends diamond:

<=2.1.8

depends hmmer:

depends importlib-metadata:

>=0.12

depends kcounter:

depends numpy:

depends prodigal-gv:

depends psutil:

depends python:

>=3.6

depends requests:

requirements:

additional platforms:

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 checkv

and update with::

   mamba update checkv

To create a new environment, run:

mamba create --name myenvname checkv

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/checkv:<tag>

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

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