recipe krocus

krocus performs multi-locus sequence typing from uncorrected long reads.

Homepage:

https://github.com/andrewjpage/krocus

License:

GPL / GPL-3.0

Recipe:

/krocus/meta.yaml

Krocus can predict a sequence type directly from uncorrected long reads, and was designed to consume read data as it is produced, providing results in minutes.

package krocus

versions:

1.0.3-0,  1.0.2-0,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.2.3-0,  0.2.2-1,  0.2.2-0

depends biopython:

>=1.68

depends pyfastaq:

>=3.14.0

depends python:

>=3

depends setuptools:

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 krocus

and update with::

   mamba update krocus

To create a new environment, run:

mamba create --name myenvname krocus

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/krocus:<tag>

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

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