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:

1.3.1-1,  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, 

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 boost-cpp:

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dbplyr:

depends r-dplyr:

depends r-matrix:

depends r-optparse:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-rcppeigen:

depends r-rcppparallel:

depends r-rhpcblasctl:

depends r-rsqlite:

depends r-skat:

depends r-spatest:

depends savvy:

depends zstd:

>=1.5.6,<1.6.0a0

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 r-saige

and update with::

   mamba update r-saige

To create a new environment, run:

mamba create --name myenvname r-saige

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/r-saige:<tag>

(see `r-saige/tags`_ for valid values for ``<tag>``)

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