recipe bioconductor-rbowtie2

An R Wrapper for Bowtie2 and AdapterRemoval

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/Rbowtie2.html

License:

GPL (>= 3)

Recipe:

/bioconductor-rbowtie2/meta.yaml

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

package bioconductor-rbowtie2

versions:

2.6.0-0,  2.4.0-1,  2.4.0-0,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0, 

2.6.0-0,  2.4.0-1,  2.4.0-0,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-magrittr:

depends zlib:

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-rbowtie2

and update with::

   mamba update bioconductor-rbowtie2

To create a new environment, run:

mamba create --name myenvname bioconductor-rbowtie2

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-rbowtie2:<tag>

(see `bioconductor-rbowtie2/tags`_ for valid values for ``<tag>``)

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Link to this page

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