recipe bioconductor-bsgenome

Software infrastructure for efficient representation of full genomes and their SNPs

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-bsgenome/meta.yaml

Links:

biotools: bsgenome, doi: 10.1038/nmeth.3252

Infrastructure shared by all the Biostrings-based genome data packages.

package bioconductor-bsgenome

versions:

1.74.0-0,  1.70.1-0,  1.68.0-0,  1.66.3-0,  1.66.1-0,  1.62.0-0,  1.60.0-0,  1.58.0-1,  1.58.0-0, 

1.74.0-0,  1.70.1-0,  1.68.0-0,  1.66.3-0,  1.66.1-0,  1.62.0-0,  1.60.0-0,  1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-0,  1.44.2-0,  1.42.0-0,  1.40.1-0,  1.38.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocio:

>=1.16.0,<1.17.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-xvector:

>=0.46.0,<0.47.0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrixstats:

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-bsgenome

and update with::

   mamba update bioconductor-bsgenome

To create a new environment, run:

mamba create --name myenvname bioconductor-bsgenome

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-bsgenome:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-bsgenome/README.html)