recipe nextstrain

Nextstrain toolchain (meta-package)

Homepage:

https://nextstrain.org

Documentation:

https://docs.nextstrain.org/

Developer docs:

https://github.com/nextstrain/

License:

The license for this meta-package is MIT; individual tools vary.

Recipe:

/nextstrain/meta.yaml

Links:

doi: 10.1093/bioinformatics/bty407

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. It includes a collection of open-source tools to aid in our understanding of pathogen spread and evolution, especially in outbreak scenarios. These tools are designed to be used with a wide range of data sources and designed to be modular so they can be replaced with your own tooling when necessary.

package nextstrain

(downloads) docker_nextstrain

versions:

20200304-2,  20200304-1,  20200304-0

depends augur:

depends auspice:

depends awscli:

depends git:

depends nextclade:

depends nextstrain-cli:

depends pip:

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 nextstrain

and update with::

   mamba update nextstrain

To create a new environment, run:

mamba create --name myenvname nextstrain

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/nextstrain:<tag>

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

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Link to this page

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