Package Recipe 'bioconductor-biocbook'

recipe bioconductor-biocbook

Write, containerize, publish and version Quarto books with Bioconductor

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/BiocBook.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-biocbook/meta.yaml

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¶

Versions:

1.8.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on r-base >=4.5,<4.6.0a0
on r-cli
on r-dplyr
on r-gert
on r-gh
on r-gitcreds
on r-glue
on r-httr
on r-pak
on r-purrr
on r-quarto
on r-renv
on r-rlang
on r-rprojroot
on r-stringr
on r-tibble
on r-usethis
on r-yaml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-biocbook

to add into an existing workspace instead, run:

pixi add bioconductor-biocbook

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-biocbook

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-biocbook

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-biocbook:<tag>

(see bioconductor-biocbook/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biocbook/README.html)