recipe nextstrain-cli

The Nextstrain command-line interface (CLI)

Homepage:

https://docs.nextstrain.org/projects/cli/

Developer docs:

https://github.com/nextstrain/cli

License:

MIT / MIT

Recipe:

/nextstrain-cli/meta.yaml

Links:

doi: 10.1093/bioinformatics/bty407

The Nextstrain command-line interface (CLI)—a program called nextstrain—aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

package nextstrain-cli

versions:

8.5.4-0,  8.5.3-0,  8.5.2-0,  8.5.1-0,  8.5.0-0,  8.2.0-0,  8.0.1-0,  8.0.0-0,  7.4.0-1, 

8.5.4-0,  8.5.3-0,  8.5.2-0,  8.5.1-0,  8.5.0-0,  8.2.0-0,  8.0.1-0,  8.0.0-0,  7.4.0-1,  7.4.0-0,  7.3.0.post1-0,  7.2.0-0,  7.1.0-0,  7.0.1-0,  7.0.0-0,  6.2.1-0,  6.2.0-1,  6.2.0-0,  6.1.0.post1-0,  6.0.3-0,  6.0.2-0,  6.0.0-0,  5.0.1-0,  5.0.0-0,  4.2.0-1,  4.2.0-0,  4.1.1-1,  4.1.1-0,  4.1.0-0,  4.0.0-0,  3.2.5-0,  3.2.4-0,  3.2.3-0,  3.2.2-0,  3.2.1-0,  3.2.0-0,  3.1.1-0,  3.0.6-0,  3.0.5-0,  3.0.3-0

depends boto3:

depends docutils:

depends fasteners:

depends fsspec:

!=2023.9.1

depends packaging:

>=3.0.0

depends pyjwt:

>=2.0.0

depends pyparsing:

depends python:

>=3.8

depends requests:

depends s3fs:

>=2021.04.0,!=2023.9.1

depends typing_extensions:

>=3.6.4

depends wcmatch:

>=6.0

depends wrapt:

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 nextstrain-cli

and update with::

   mamba update nextstrain-cli

To create a new environment, run:

mamba create --name myenvname nextstrain-cli

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-cli:<tag>

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

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