recipe shigeifinder

Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies

Homepage:

https://github.com/LanLab/ShigEiFinder

License:

GPL3

Recipe:

/shigeifinder/meta.yaml

package shigeifinder

versions:

1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.2.0-0,  1.1.0-0

depends blast:

>=2.9.0

depends bwa:

>=0.7.17

depends python:

>=3.7

depends samtools:

>=1.10

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 shigeifinder

and update with::

   mamba update shigeifinder

To create a new environment, run:

mamba create --name myenvname shigeifinder

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/shigeifinder:<tag>

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

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