Package Recipe 'bioconductor-anvil'

recipe bioconductor-anvil

Bioconductor on the AnVIL compute environment

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/AnVIL.html
License:: Artistic-2.0
Recipe:: /bioconductor-anvil/meta.yaml

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

package bioconductor-anvil¶

Versions:

1.22.3-0, 1.18.0-0, 1.14.0-0, 1.12.3-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.2.0-0,

1.22.3-0, 1.18.0-0, 1.14.0-0, 1.12.3-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.2.0-0, 1.0.3-0

Depends:

on bioconductor-anvilbase >=1.4.0,<1.5.0
on bioconductor-biocbaseutils >=1.12.0,<1.13.0
on bioconductor-gcptools >=1.0.0,<1.1.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-dt
on r-futile.logger
on r-htmltools
on r-httr
on r-jsonlite
on r-miniui
on r-rapiclient
on r-shiny
on r-tibble
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-anvil

to add into an existing workspace instead, run:

pixi add bioconductor-anvil

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-anvil

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-anvil

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-anvil:<tag>

(see bioconductor-anvil/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-anvil/README.html)