recipe scagaire

Scagaire allows you to take in gene predictions from a metagenomic sample and filter them by bacterial/pathogenic species

Homepage:

https://github.com/quadram-institute-bioscience/scagaire

License:

GPLv3

Recipe:

/scagaire/meta.yaml

package scagaire

(downloads) docker_scagaire

versions:

0.0.4-0

depends biopython:

>=1.68

depends mash:

depends python:

>=3

depends pyyaml:

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 scagaire

and update with::

   mamba update scagaire

To create a new environment, run:

mamba create --name myenvname scagaire

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/scagaire:<tag>

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

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Link to this page

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

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