recipe regain-cli

Bayesian-network pipeline for ARG/virulence co-occurrence analysis.

Homepage:

https://github.com/ERBringHorvath/regain_CLI

License:

MIT

Recipe:

/regain-cli/meta.yaml

ReGAIN is a reproducible CLI for quantifying co-occurrence among bacterial antibiotic/heavy metal resistance and virulence genes using Bayesian network structure learning (bnlearn/gRain) and post-hoc metrics. It includes dataset curation, visualization, and multivariate analysis.

package regain-cli

versions:

1.6.3-0,  1.6.2-0

depends bioconductor-graph:

depends biopython:

depends blast:

depends ncbi-amrfinderplus:

depends pandas:

depends python:

>=3.10

depends r-ape:

depends r-base:

>=4.4

depends r-bnlearn:

depends r-cluster:

depends r-compositions:

depends r-doparallel:

depends r-dplyr:

depends r-ellipse:

depends r-foreach:

depends r-ggplot2:

depends r-ggraph:

depends r-ggrepel:

depends r-grain:

depends r-igraph:

depends r-optparse:

depends r-pbapply:

depends r-progressr:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

depends r-tibble:

depends r-tidygraph:

depends r-tidyr:

depends r-vegan:

depends r-visnetwork:

requirements:

additional platforms:

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 regain-cli

and update with::

   mamba update regain-cli

To create a new environment, run:

mamba create --name myenvname regain-cli

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/regain-cli:<tag>

(see `regain-cli/tags`_ for valid values for ``<tag>``)

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