recipe bioconductor-rbowtie

R bowtie wrapper

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/Rbowtie.html

License:

Artistic-2.0 | file LICENSE

Recipe:

/bioconductor-rbowtie/meta.yaml

Links:

biotools: rbowtie, doi: 10.1038/nmeth.3252

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

package bioconductor-rbowtie

(downloads) docker_bioconductor-rbowtie

versions:
1.46.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-2,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0, 

1.46.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-2,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends r-base:

>=4.4,<4.5.0a0

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-rbowtie

and update with::

   mamba update bioconductor-rbowtie

To create a new environment, run:

mamba create --name myenvname bioconductor-rbowtie

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-rbowtie:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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