recipe abritamr

Running AMRFinderPlus for MDU

Homepage:

https://github.com/MDU-PHL/abritamr

License:

GPL3 / GPL-3.0-only

Recipe:

/abritamr/meta.yaml

package abritamr

(downloads) docker_abritamr

versions:
1.0.14-1,  1.0.14-0,  1.0.13-0,  1.0.12-0,  1.0.11-0,  1.0.10-0,  1.0.9-0,  1.0.8-0,  1.0.7-1, 

1.0.14-1,  1.0.14-0,  1.0.13-0,  1.0.12-0,  1.0.11-0,  1.0.10-0,  1.0.9-0,  1.0.8-0,  1.0.7-1,  1.0.7-0,  1.0.6-0,  1.0.4-0,  1.0.3-0,  1.0.0-0,  0.2.2-0,  0.1.0-0

depends blast:

depends hmmer:

depends libcurl:

depends ncbi-amrfinderplus:

3.10.42.*

depends pandas:

>1.4*

depends parallel:

depends python:

depends xlsxwriter:

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 abritamr

and update with::

   mamba update abritamr

To create a new environment, run:

mamba create --name myenvname abritamr

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/abritamr:<tag>

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

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Render an install-with-bioconda badge with the following MarkDown:

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