recipe virmet

A pipeline for viral metagenomics

Homepage:

https://github.com/medvir/VirMet

Documentation:

https://medvir.github.io/VirMet/

License:

MIT / MIT

Recipe:

/virmet/meta.yaml

VirMet is a Python package for viral metagenomics analysis in clinical applications. It includes command-line utilities and depends on common bioinformatics tools.

package virmet

(downloads) docker_virmet

versions:
2.0.0-0,  1.1.1-0,  v1.1.1-5,  v1.1.1-4,  v1.1.1-3,  v1.1.1-2,  v1.1.1-1,  v1.1.1-0,  v1.1-2, 

2.0.0-0,  1.1.1-0,  v1.1.1-5,  v1.1.1-4,  v1.1.1-3,  v1.1.1-2,  v1.1.1-1,  v1.1.1-0,  v1.1-2,  v1.1-1,  v1.1-0,  v1.0-0

depends biopython:

depends blast:

>=2.3

depends bwa:

depends fastp:

depends htslib:

depends kraken2:

>=2.1.6

depends ncbi-datasets-cli:

depends numpy:

depends pandas:

depends python:

>=3.9

depends r-ggplot2:

depends requests:

depends samtools:

>=1.3

depends seqkit:

depends seqtk:

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 virmet

and update with::

   mamba update virmet

To create a new environment, run:

mamba create --name myenvname virmet

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/virmet:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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