recipe bioconductor-metascope

Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/MetaScope.html

License:

GPL (>= 3)

Recipe:

/bioconductor-metascope/meta.yaml

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

package bioconductor-metascope

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-rbowtie2:

>=2.8.0,<2.9.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-matrix:

depends r-qlcmatrix:

depends r-readr:

depends r-rlang:

depends r-stringr:

depends r-taxize:

depends r-tidyr:

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 bioconductor-metascope

and update with::

   mamba update bioconductor-metascope

To create a new environment, run:

mamba create --name myenvname bioconductor-metascope

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-metascope:<tag>

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

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