recipe mykrobe

Antibiotic resistance prediction in minutes

Homepage:

https://github.com/Mykrobe-tools/mykrobe

License:

MIT

Recipe:

/mykrobe/meta.yaml

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

package mykrobe

versions:

0.13.0-4,  0.13.0-3,  0.13.0-2,  0.13.0-1,  0.13.0-0,  0.12.2-1,  0.12.2-0,  0.12.1-2,  0.12.1-1, 

0.13.0-4,  0.13.0-3,  0.13.0-2,  0.13.0-1,  0.13.0-0,  0.12.2-1,  0.12.2-0,  0.12.1-2,  0.12.1-1,  0.12.1-0,  0.12.0-0,  0.11.0-1,  0.11.0-0,  0.10.0-1,  0.10.0-0,  0.9.0-3,  0.9.0-2,  0.9.0-1,  0.9.0-0,  0.8.2-1,  0.8.2-0,  0.8.1-0,  0.8.0-1,  0.8.0-0,  0.7.0-5,  0.7.0-4,  0.7.0-3,  0.7.0-2,  0.7.0-0,  0.6.1-3,  0.6.1-2,  0.6.1-1,  0.6.1-0,  0.5.6-1,  0.5.6-0

depends anytree:

depends biopython:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends mongodb:

>3.0

depends mongoengine:

>=0.18.0

depends numpy:

>=1.22.4,<2.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends pyvcf3:

>=1.0.3

depends requests:

depends setuptools:

depends wget:

depends zlib:

requirements:

additional platforms:

linux-aarch64

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 mykrobe

and update with::

   mamba update mykrobe

To create a new environment, run:

mamba create --name myenvname mykrobe

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/mykrobe:<tag>

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

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