recipe bioconductor-genomicfiles

Distributed computing by file or by range

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/GenomicFiles.html

License:

Artistic-2.0

Recipe:

/bioconductor-genomicfiles/meta.yaml

Links:

biotools: genomicfiles, doi: 10.1038/nmeth.3252

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

package bioconductor-genomicfiles

versions:

1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0, 

1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

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-genomicfiles

and update with::

   mamba update bioconductor-genomicfiles

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicfiles

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-genomicfiles:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-genomicfiles/README.html)