recipe bioconductor-beachmat.hdf5

beachmat bindings for HDF5-backed matrices

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/beachmat.hdf5.html

License:

GPL-3

Recipe:

/bioconductor-beachmat.hdf5/meta.yaml

Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

package bioconductor-beachmat.hdf5

versions:

1.0.0-0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0a0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0a0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0a0

depends bioconductor-rhdf5lib:

>=1.24.0,<1.25.0

depends bioconductor-rhdf5lib:

>=1.24.0,<1.25.0a0

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-rcpp:

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.hdf5

and update with::

   mamba update bioconductor-beachmat.hdf5

To create a new environment, run:

mamba create --name myenvname bioconductor-beachmat.hdf5

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.hdf5:<tag>

(see `bioconductor-beachmat.hdf5/tags`_ for valid values for ``<tag>``)

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