recipe bioconductor-annotationhub

Client to access AnnotationHub resources

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-annotationhub/meta.yaml

Links:

biotools: annotationhub, doi: 10.1038/nmeth.3252

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

package bioconductor-annotationhub

versions:

3.8.0-0,  3.6.0-0,  3.2.0-0,  3.0.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1, 

3.8.0-0,  3.6.0-0,  3.2.0-0,  3.0.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.5-0,  2.14.2-0,  2.12.1-0,  2.10.1-0,  2.10.0-0,  2.8.2-0,  2.6.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocversion:

>=3.17.0,<3.18.0

depends bioconductor-interactivedisplaybase:

>=1.38.0,<1.39.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-curl:

depends r-dplyr:

depends r-httr:

depends r-rappdirs:

depends r-rsqlite:

depends r-yaml:

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-annotationhub

and update with::

   mamba update bioconductor-annotationhub

To create a new environment, run:

mamba create --name myenvname bioconductor-annotationhub

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-annotationhub:<tag>

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

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