recipe salmid

Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).

Homepage:

https://github.com/hcdenbakker/SalmID

License:

MIT

Recipe:

/salmid/meta.yaml

Links:

DOI: 10.5281/zenodo.1409766

package salmid

(downloads) docker_salmid

versions:

0.1.23-0

depends python:

>=3

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 salmid

and update with::

   mamba update salmid

To create a new environment, run:

mamba create --name myenvname salmid

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/salmid:<tag>

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

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Link to this page

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