recipe bioconductor-eupathdb

Provides access to pathogen annotation resources available on EuPathDB databases

Homepage:

https://bioconductor.org/packages/3.17/data/annotation/html/EuPathDB.html

License:

Artistic-2.0

Recipe:

/bioconductor-eupathdb/meta.yaml

Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.

package bioconductor-eupathdb

versions:

1.0.1-11,  1.0.1-10,  1.0.1-9,  1.0.1-8,  1.0.1-7,  1.0.1-6,  1.0.1-5,  1.0.1-4,  1.0.1-3, 

1.0.1-11,  1.0.1-10,  1.0.1-9,  1.0.1-8,  1.0.1-7,  1.0.1-6,  1.0.1-5,  1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-annotationhubdata:

>=1.30.0,<1.31.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-genomeinfodbdata:

>=1.2.0,<1.3.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

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-eupathdb

and update with::

   mamba update bioconductor-eupathdb

To create a new environment, run:

mamba create --name myenvname bioconductor-eupathdb

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-eupathdb:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-eupathdb/README.html)