recipe staramr

Scan genome contigs against the ResFinder and PointFinder databases

Homepage:

https://github.com/phac-nml/staramr

License:

APACHE / Apache Software License

Recipe:

/staramr/meta.yaml

package staramr

versions:

0.10.0-0,  0.9.1-0,  0.9.0-0,  0.8.0-1,  0.8.0-0,  0.7.2-1,  0.7.2-0,  0.7.1-1,  0.7.1-0, 

0.10.0-0,  0.9.1-0,  0.9.0-0,  0.8.0-1,  0.8.0-0,  0.7.2-1,  0.7.2-0,  0.7.1-1,  0.7.1-0,  0.7.0-0,  0.6.1-0,  0.6.0-0,  0.5.1-0,  0.5.0-0,  0.4.0-2,  0.4.0-1,  0.4.0-0,  0.3.0-0,  0.2.2-0,  0.2.1-0,  0.2.0-1,  0.2.0-0,  0.1.0-0

depends biopython:

>=1.70

depends blast:

>=2.2.31

depends coloredlogs:

>=10.0

depends file:

depends git:

depends gitpython:

>=2.1.3

depends green:

>=2.13.0

depends mlst:

depends numpy:

>=1.12.1

depends pandas:

>=0.23.0

depends python:

>=3

depends xlsxwriter:

>=1.0.2

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 staramr

and update with::

   mamba update staramr

To create a new environment, run:

mamba create --name myenvname staramr

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/staramr:<tag>

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

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