recipe bioconductor-organismdbi

Software to enable the smooth interfacing of different database packages

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/OrganismDbi.html

License:

Artistic-2.0

Recipe:

/bioconductor-organismdbi/meta.yaml

Links:

biotools: organismdbi, doi: 10.1038/nmeth.3252

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

package bioconductor-organismdbi

versions:

1.48.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0, 

1.48.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.1-0,  1.14.1-0,  1.12.1-0,  1.12.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-graph:

>=1.84.0,<1.85.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rbgl:

>=1.82.0,<1.83.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-txdbmaker:

>=1.2.0,<1.3.0

depends r-base:

>=4.4,<4.5.0a0

depends r-biocmanager:

depends r-dbi:

requirements:

additional platforms:

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-organismdbi

and update with::

   mamba update bioconductor-organismdbi

To create a new environment, run:

mamba create --name myenvname bioconductor-organismdbi

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-organismdbi:<tag>

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

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