recipe bioconductor-gmapr

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/gmapR.html

License

Artistic-2.0

Recipe

/bioconductor-gmapr/meta.yaml

package bioconductor-gmapr

Versions

1.26.0-1, 1.24.1-0

Depends

• bioconductor-biobase >=2.44.0,<2.45.0

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-biostrings >=2.52.0,<2.53.0

• bioconductor-bsgenome >=1.52.0,<1.53.0

• bioconductor-genomeinfodb >=1.20.0,<1.21.0

• bioconductor-genomicalignments >=1.20.0,<1.21.0

• bioconductor-genomicfeatures >=1.36.0,<1.37.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-rsamtools >=2.0.0,<2.1.0

• bioconductor-rtracklayer >=1.44.0,<1.45.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-variantannotation >=1.30.0,<1.31.0

• libgcc-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

Required By

• bioconductor-mtseeker

• bioconductor-htseqgenie

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)