recipe bioconductor-systempiperdata

systemPipeRdata: Workflow templates and sample data

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/systemPipeRdata.html

License:

Artistic-2.0

Recipe:

/bioconductor-systempiperdata/meta.yaml

systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette.

package bioconductor-systempiperdata

(downloads) docker_bioconductor-systempiperdata

versions:
2.4.0-0,  2.2.0-0,  1.22.3-0,  1.22.0-0,  1.20.0-0,  1.18.1-0,  1.18.0-0,  1.17.4-0,  1.16.1-0, 

2.4.0-0,  2.2.0-0,  1.22.3-0,  1.22.0-0,  1.20.0-0,  1.18.1-0,  1.18.0-0,  1.17.4-0,  1.16.1-0,  1.14.0-0,  1.12.0-1,  1.10.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-data-packages:

>=20230706

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-jsonlite:

depends r-remotes:

requirements:

Installation

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-systempiperdata

and update with::

   mamba update bioconductor-systempiperdata

To create a new environment, run:

mamba create --name myenvname bioconductor-systempiperdata

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 quay.io/biocontainers/bioconductor-systempiperdata:<tag>

(see `bioconductor-systempiperdata/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda 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-systempiperdata/README.html)