recipe r-whopgenome

Provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

Homepage:

https://CRAN.R-project.org/package=WhopGenome

License:

GPL3 / GPL (>= 2)

Recipe:

/r-whopgenome/meta.yaml

package r-whopgenome

(downloads) docker_r-whopgenome

versions:
0.9.7-9,  0.9.7-8,  0.9.7-7,  0.9.7-6,  0.9.7-5,  0.9.7-4,  0.9.7-3,  0.9.7-2,  0.9.7-1, 

0.9.7-9,  0.9.7-8,  0.9.7-7,  0.9.7-6,  0.9.7-5,  0.9.7-4,  0.9.7-3,  0.9.7-2,  0.9.7-1,  0.9.7-0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

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 r-whopgenome

and update with::

   mamba update r-whopgenome

To create a new environment, run:

mamba create --name myenvname r-whopgenome

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/r-whopgenome:<tag>

(see `r-whopgenome/tags`_ for valid values for ``<tag>``)

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Link to this page

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