recipe nirvana

Clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs)

Homepage:

https://github.com/Illumina/Nirvana

Documentation:

https://illumina.github.io/NirvanaDocumentation/

License:

GPL / GPL-3.0-only

Recipe:

/nirvana/meta.yaml

Nirvana provides clinical-grade annotation of genomic variants. It processes VCF files and outputs structured JSON representations of variant annotations. While this open-source version is no longer actively maintained, users are directed to Illumina Connected Annotations for the current maintained version.

package nirvana

versions:

3.18.1-1,  3.18.1-0

depends dotnet-runtime:

>=6.0,<7.0a0

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 nirvana

and update with::

   mamba update nirvana

To create a new environment, run:

mamba create --name myenvname nirvana

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/nirvana:<tag>

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

Notes

This tool is no longer actively maintained. Users should consider Illumina Connected Annotations for the current maintained version.

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