recipe mtb-snp-it

SNP-IT: Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex.

Homepage:

https://github.com/samlipworth/snpit

License:

MIT

Recipe:

/mtb-snp-it/meta.yaml

Links:

doi: 10.3201/eid2503.180894

Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex. Based on code originally written by Samuel Lipworth and turned into a package by Philip Fowler.

SNP-IT allows rapid Mycobacterial speciation of VCF or FASTA files aligned to NC000962 (H37rV).

package mtb-snp-it

(downloads) docker_mtb-snp-it

versions:

1.1-1,  1.1-0,  0.1.0-0

depends biopython:

depends python:

depends pyvcf:

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 mtb-snp-it

and update with::

   mamba update mtb-snp-it

To create a new environment, run:

mamba create --name myenvname mtb-snp-it

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/mtb-snp-it:<tag>

(see `mtb-snp-it/tags`_ for valid values for ``<tag>``)

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