Package Recipe 'bioconductor-anvilworkflow'

recipe bioconductor-anvilworkflow

Run workflows implemented in Terra/AnVIL workspace

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

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.

package bioconductor-anvilworkflow¶

Versions:

1.10.0-0, 1.6.0-0, 1.2.0-0, 1.0.1-0

Depends:

on bioconductor-anvil >=1.22.0,<1.23.0
on bioconductor-anvilbase >=1.4.0,<1.5.0
on bioconductor-anvilgcp >=1.4.0,<1.5.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-httr
on r-jsonlite
on r-plyr
on r-rlang
on r-stringr
on r-tibble
on r-tidyr

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-anvilworkflow

to add into an existing workspace instead, run:

pixi add bioconductor-anvilworkflow

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-anvilworkflow

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-anvilworkflow

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-anvilworkflow:<tag>

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