recipe bioconductor-anvilpublish

Publish Packages and Other Resources to AnVIL Workspaces






Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.

package bioconductor-anvilpublish

(downloads) docker_bioconductor-anvilpublish



depends bioconductor-anvil:


depends r-base:


depends r-httr:

depends r-jsonlite:

depends r-readr:

depends r-rmarkdown:

depends r-whisker:

depends r-yaml:



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-anvilpublish

and update with::

   mamba update bioconductor-anvilpublish

To create a new environment, run:

mamba create --name myenvname bioconductor-anvilpublish

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

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