recipe bioconductor-gmapr

An R interface to the GMAP/GSNAP/GSTRUCT suite

Homepage

https://bioconductor.org/packages/3.10/bioc/html/gmapR.html

License

Artistic-2.0

Recipe

/bioconductor-gmapr/meta.yaml

GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

package bioconductor-gmapr

Versions

1.28.0-0, 1.26.0-1, 1.24.1-0

Depends

• bioconductor-biobase >=2.46.0,<2.47.0

• bioconductor-biocgenerics >=0.32.0,<0.33.0

• bioconductor-biocparallel >=1.20.0,<1.21.0

• bioconductor-biostrings >=2.54.0,<2.55.0

• bioconductor-bsgenome >=1.54.0,<1.55.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicalignments >=1.22.0,<1.23.0

• bioconductor-genomicfeatures >=1.38.0,<1.39.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-variantannotation >=1.32.0,<1.33.0

• libgcc-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

Required By

• bioconductor-mtseeker

• bioconductor-htseqgenie

• bioconductor-mmappr2

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-gmapr

and update with:

conda update bioconductor-gmapr

or use the docker container:

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

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

Link to this page

Render an 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-gmapr/README.html)