recipe uscdc-datasets-sars-cov-2

Benchmark datasets for WGS analysis of SARS-CoV-2

Homepage:

https://github.com/CDCgov/datasets-sars-cov-2

License:

Apache-2.0

Recipe:

/uscdc-datasets-sars-cov-2/meta.yaml

package uscdc-datasets-sars-cov-2

versions:

0.7.2-0,  0.7.1-0,  0.7-0,  0.6.3-0,  0.6.2-0,  0.5.3-0,  0.4-0,  0.3-0

depends coreutils:

depends entrez-direct:

depends make:

depends perl:

depends sra-tools:

depends wget:

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 uscdc-datasets-sars-cov-2

and update with::

   mamba update uscdc-datasets-sars-cov-2

To create a new environment, run:

mamba create --name myenvname uscdc-datasets-sars-cov-2

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/uscdc-datasets-sars-cov-2:<tag>

(see `uscdc-datasets-sars-cov-2/tags`_ for valid values for ``<tag>``)

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