recipe bioconductor-rbec

Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Rbec.html

License:

LGPL-3

Recipe:

/bioconductor-rbec/meta.yaml

Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.

package bioconductor-rbec

versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-dada2:

>=1.34.0,<1.35.0

depends bioconductor-dada2:

>=1.34.0,<1.35.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-doparallel:

depends r-foreach:

depends r-ggplot2:

depends r-rcpp:

>=1.0.6

depends r-readr:

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 bioconductor-rbec

and update with::

   mamba update bioconductor-rbec

To create a new environment, run:

mamba create --name myenvname bioconductor-rbec

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/bioconductor-rbec:<tag>

(see `bioconductor-rbec/tags`_ for valid values for ``<tag>``)

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