recipe bioconductor-biocbook

Write, containerize, publish and version Quarto books with Bioconductor






A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, …) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

package bioconductor-biocbook

(downloads) docker_bioconductor-biocbook



depends bioconductor-biocgenerics:


depends r-available:

depends r-base:


depends r-cli:

depends r-dplyr:

depends r-gert:

depends r-gh:

depends r-gitcreds:

depends r-glue:

depends r-httr:

depends r-purrr:

depends r-quarto:

depends r-renv:

depends r-rlang:

depends r-rprojroot:

depends r-stringr:

depends r-tibble:

depends r-usethis:

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-biocbook

and update with::

   mamba update bioconductor-biocbook

To create a new environment, run:

mamba create --name myenvname bioconductor-biocbook

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

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