recipe bioconductor-girafe

Genome Intervals and Read Alignments for Functional Exploration

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/girafe.html

License:

Artistic-2.0

Recipe:

/bioconductor-girafe/meta.yaml

Links:

biotools: girafe

The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.

package bioconductor-girafe

versions:

1.52.0-0,  1.50.0-1,  1.50.0-0,  1.46.0-2,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0, 

1.52.0-0,  1.50.0-1,  1.50.0-0,  1.46.0-2,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomeintervals:

>=1.56.0,<1.57.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-shortread:

>=1.58.0,<1.59.0

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-intervals:

>=0.13.1

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-girafe

and update with::

   mamba update bioconductor-girafe

To create a new environment, run:

mamba create --name myenvname bioconductor-girafe

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-girafe:<tag>

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

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