recipe genotyphi

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

Homepage:

https://github.com/typhoidgenomics/genotyphi

License:

GPL3

Recipe:

/genotyphi/meta.yaml

package genotyphi

versions:

2.0-1,  2.0-0,  1.9.1-1,  1.9.1-0,  1.9.0-0,  1.8.0-0,  1.7.1-0

depends bcftools:

>=1.1

depends pandas:

depends python:

<3

depends samtools:

>=1.1

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 genotyphi

and update with::

   mamba update genotyphi

To create a new environment, run:

mamba create --name myenvname genotyphi

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/genotyphi:<tag>

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

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