Package Recipe 'r-saige'

recipe r-saige

SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016)

Homepage:: https://github.com/saigegit/SAIGE
License:: GPL3 / GPL-3.0-only
Recipe:: /r-saige/meta.yaml

SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400000).

package r-saige¶

Versions:

1.3.1-4, 1.3.1-3, 1.3.1-2, 1.3.1-1, 1.3.1-0, 1.2.0-0, 1.1.9-3, 1.1.9-2, 1.1.9-1,

1.3.1-4, 1.3.1-3, 1.3.1-2, 1.3.1-1, 1.3.1-0, 1.2.0-0, 1.1.9-3, 1.1.9-2, 1.1.9-1, 1.1.9-0, 1.1.8-0, 0.45.0-5, 0.45.0-4, 0.45.0-3, 0.45.0-2, 0.45.0-0, 0.44.6.5-3, 0.44.6.5-2, 0.44.6.5-1, 0.44.6.5-0, 0.44.6.2-0, 0.44.6.1-0, 0.44.6-0, 0.44.5-1, 0.44.5-0, 0.44.2-0, 0.44.1-0, 0.44.0-0, 0.43.3-0, 0.43.0-0, 0.42.1-1, 0.42.1-0, 0.42.0-1, 0.42.0-0, 0.39.0-1, 0.39.0-0, 0.35.8.8-2, 0.35.8.8-1, 0.35.8.8-0

Depends:

on boost-cpp
on libblas >=3.9.0,<4.0a0
on libgcc >=13
on liblapack >=3.9.0,<4.0a0
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on r-base >=4.4,<4.5.0a0
on r-data.table
on r-dbplyr
on r-dplyr
on r-matrix
on r-optparse
on r-rcpp
on r-rcpparmadillo
on r-rcppeigen
on r-rcppparallel
on r-rhpcblasctl
on r-rsqlite
on r-skat
on r-spatest
on savvy >=2.1.0,<3.0a0
on superlu >=7.0.1,<7.1.0a0
on zstd >=1.5.7,<1.6.0a0

Additional platforms:

linux-aarch64, osx-arm64

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 r-saige

to add into an existing workspace instead, run:

pixi add r-saige

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 r-saige

Alternatively, to install into a new environment, run:

conda create -n envname r-saige

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/r-saige:<tag>

(see r-saige/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/r-saige/README.html)