recipe bioconductor-alabaster.vcf

Save and Load Variant Data to/from File

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/alabaster.vcf.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-alabaster.vcf/meta.yaml

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

package bioconductor-alabaster.vcf

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-alabaster.base:

>=1.2.0,<1.3.0

depends bioconductor-alabaster.se:

>=1.2.0,<1.3.0

depends bioconductor-alabaster.string:

>=1.2.0,<1.3.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

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-alabaster.vcf

and update with::

   mamba update bioconductor-alabaster.vcf

To create a new environment, run:

mamba create --name myenvname bioconductor-alabaster.vcf

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-alabaster.vcf:<tag>

(see `bioconductor-alabaster.vcf/tags`_ for valid values for ``<tag>``)

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