recipe bioconductor-rbowtie2

An R Wrapper for Bowtie2 and AdapterRemoval

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Rbowtie2.html

License:

GPL (>= 3)

Recipe:

/bioconductor-rbowtie2/meta.yaml

Links:

biotools: rbowtie2

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

(downloads) docker_bioconductor-rbowtie2

Versions:
2.16.0-0,  2.12.3-0,  2.8.0-1,  2.8.0-0,  2.6.0-0,  2.4.0-1,  2.4.0-0,  2.0.0-2,  2.0.0-1, 

2.16.0-0,  2.12.3-0,  2.8.0-1,  2.8.0-0,  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:

  • on bioconductor-rsamtools >=2.26.0,<2.27.0

  • on bioconductor-rsamtools >=2.26.0,<2.27.0a0

  • on libblas >=3.9.0,<4.0a0

  • on libgcc >=14

  • on liblapack >=3.9.0,<4.0a0

  • on liblzma >=5.8.2,<6.0a0

  • on libstdcxx >=14

  • on libzlib >=1.3.1,<2.0a0

  • on r-base >=4.5,<4.6.0a0

  • on r-magrittr

Additional platforms:
linux-aarch64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rbowtie2

to add into an existing workspace instead, run:

pixi add bioconductor-rbowtie2

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rbowtie2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rbowtie2

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-rbowtie2:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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