recipe grimer

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard

Homepage:

https://github.com/pirovc/grimer

License:

MIT / MIT License

Recipe:

/grimer/meta.yaml

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

package grimer

versions:

1.1.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-decontam:

1.10.0

depends biom-format:

>=2.1.10

depends bokeh:

2.2.3

depends jinja2:

3.0.3

depends markdown:

depends multitax:

>=1.2.1

depends numpy:

depends pandas:

depends python:

>=3.5

depends r-base:

>=4.0.0

depends r-optparse:

1.6.6

depends scikit-bio:

>=0.5.6

depends scipy:

>=1.6.0

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 grimer

and update with::

   mamba update grimer

To create a new environment, run:

mamba create --name myenvname grimer

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/grimer:<tag>

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

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