recipe srst2

Short Read Sequence Typing for Bacterial Pathogens

Homepage:

https://github.com/katholt/srst2

License:

BSD

Recipe:

/srst2/meta.yaml

package srst2

versions:

0.2.0-4,  0.2.0-3,  0.2.0-2,  0.2.0-1,  0.2.0-0,  0.1.6-1,  0.1.6-0,  0.1.4.6-1,  0.1.4.6-0

depends bowtie2:

<=2.2.9

depends numpy:

>=1.7.1

depends python:

<3

depends samtools:

0.1.18

depends scipy:

>=0.12.0

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 srst2

and update with::

   mamba update srst2

To create a new environment, run:

mamba create --name myenvname srst2

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/srst2:<tag>

(see `srst2/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/srst2/README.html)