recipe bioconductor-ahmassbank

MassBank Annotation Resources for AnnotationHub






Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds' ions. MassBank data is retrieved from and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.

package bioconductor-ahmassbank

(downloads) docker_bioconductor-ahmassbank



depends bioconductor-annotationhubdata:


depends r-base:




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-ahmassbank

and update with::

   mamba update bioconductor-ahmassbank

To create a new environment, run:

mamba create --name myenvname bioconductor-ahmassbank

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-ahmassbank/tags`_ for valid values for ``<tag>``)

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