recipe bioconductor-customcmpdb

Customize and Query Compound Annotation Database






This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

package bioconductor-customcmpdb

(downloads) docker_bioconductor-customcmpdb



depends bioconductor-annotationhub:


depends bioconductor-biocfilecache:


depends bioconductor-chemminer:


depends r-base:


depends r-rappdirs:

depends r-rsqlite:

depends r-xml:



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-customcmpdb

and update with::

   mamba update bioconductor-customcmpdb

To create a new environment, run:

mamba create --name myenvname bioconductor-customcmpdb

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<tag>

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

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