recipe bioconductor-beachmat

Compiling Bioconductor to Handle Each Matrix Type

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/beachmat.html

License:

GPL-3.0-only

Recipe:

/bioconductor-beachmat/meta.yaml

Links:

biotools: beachmat

Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.

package bioconductor-beachmat

versions:

2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.0-2,  2.10.0-1,  2.10.0-0,  2.8.0-0, 

2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.0-2,  2.10.0-1,  2.10.0-0,  2.8.0-0,  2.6.4-1,  2.6.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1,  1.4.0-1,  1.4.0-0,  1.2.1-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0a0

depends bioconductor-sparsearray:

>=1.2.0,<1.3.0

depends bioconductor-sparsearray:

>=1.2.2,<1.3.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-rcpp:

depends tapi:

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-beachmat

and update with::

   mamba update bioconductor-beachmat

To create a new environment, run:

mamba create --name myenvname bioconductor-beachmat

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-beachmat:<tag>

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

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Link to this page

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