- recipe bioconductor-gmapr
An R interface to the GMAP/GSNAP/GSTRUCT suite
- Homepage:
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: 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.
- package bioconductor-gmapr¶
- versions:
1.48.0-0,1.44.0-1,1.44.0-0,1.42.0-0,1.40.0-1,1.40.0-0,1.36.0-2,1.36.0-1,1.36.0-0,1.48.0-0,1.44.0-1,1.44.0-0,1.42.0-0,1.40.0-1,1.40.0-0,1.36.0-2,1.36.0-1,1.36.0-0,1.34.0-0,1.32.0-2,1.32.0-1,1.32.0-0,1.30.0-0,1.28.0-0,1.26.0-1,1.24.1-0- depends bioconductor-biobase:
>=2.66.0,<2.67.0- depends bioconductor-biobase:
>=2.66.0,<2.67.0a0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0a0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0a0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0a0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-variantannotation:
>=1.52.0,<1.53.0- depends bioconductor-variantannotation:
>=1.52.0,<1.53.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends libzlib:
>=1.3.1,<2.0a0- depends r-base:
>=4.4,<4.5.0a0- requirements:
- additional platforms:
linux-aarch64
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-gmapr and update with:: mamba update bioconductor-gmapr
To create a new environment, run:
mamba create --name myenvname bioconductor-gmapr
with
myenvnamebeing 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-gmapr:<tag> (see `bioconductor-gmapr/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-gmapr/README.html)
