recipe nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Homepage:

https://github.com/nextstrain/nextclade

Documentation:

https://docs.nextstrain.org/projects/nextclade/en/stable/

License:

MIT / MIT

Recipe:

/nextclade/meta.yaml

Links:

doi: 10.21105/joss.03773

package nextclade

(downloads) docker_nextclade

versions:
3.9.1-0,  3.9.0-0,  3.8.2-0,  3.8.1-0,  3.8.0-2,  3.8.0-1,  3.8.0-0,  3.7.4-0,  3.7.3-0, 

3.9.1-0,  3.9.0-0,  3.8.2-0,  3.8.1-0,  3.8.0-2,  3.8.0-1,  3.8.0-0,  3.7.4-0,  3.7.3-0,  3.7.1-0,  3.7.0-0,  3.6.0-0,  3.5.0-0,  3.4.0-0,  3.3.1-2,  3.3.1-1,  3.3.1-0,  3.3.0-1,  3.3.0-0,  3.2.1-0,  3.2.0-0,  3.1.0-0,  3.0.1-0,  3.0.0-0,  2.14.0-2,  2.14.0-1,  2.14.0-0,  2.13.1-0,  2.13.0-0,  2.12.0-0,  2.11.0-0,  2.10.1-0,  2.9.1-0,  2.9.0-1,  2.9.0-0,  2.8.0-0,  2.7.0-0,  2.6.0-0,  2.5.0-0,  2.4.0-0,  2.3.1-0,  2.3.0-0,  2.2.0-0,  2.1.0-0,  2.0.0-0,  1.11.0-0,  1.10.3-0,  1.10.2-0,  1.10.1-0,  1.10.0-0,  1.9.0-0,  1.8.1-0,  1.8.0-0,  1.7.0-0,  1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.5-0,  1.4.4-0,  1.4.1-0,  1.4.0-0,  1.3.0-0,  1.2.3-1,  1.2.3-0,  1.2.1-0,  1.2.0-0,  1.1.0-0

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 nextclade

and update with::

   mamba update nextclade

To create a new environment, run:

mamba create --name myenvname nextclade

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/nextclade:<tag>

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

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

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