recipe bioconductor-ompbam

C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-ompbam/meta.yaml

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

package bioconductor-ompbam

(downloads) docker_bioconductor-ompbam

versions:

1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0a0

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-ompbam

and update with::

   mamba update bioconductor-ompbam

To create a new environment, run:

mamba create --name myenvname bioconductor-ompbam

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-ompbam:<tag>

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

Download stats

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-ompbam/README.html)