recipe bioconductor-vcfarray

Representing on-disk / remote VCF files as array-like objects

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/VCFArray.html

License:

GPL-3

Recipe:

/bioconductor-vcfarray/meta.yaml

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

package bioconductor-vcfarray

versions:

1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.3-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-delayedarray:

>=0.26.0,<0.27.0

depends bioconductor-genomicfiles:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

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 bioconductor-vcfarray

and update with::

   mamba update bioconductor-vcfarray

To create a new environment, run:

mamba create --name myenvname bioconductor-vcfarray

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/bioconductor-vcfarray:<tag>

(see `bioconductor-vcfarray/tags`_ for valid values for ``<tag>``)

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