recipe bioconductor-genomicalignments

Representation and manipulation of short genomic alignments

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-genomicalignments/meta.yaml

Links:

biotools: genomicalignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

package bioconductor-genomicalignments

versions:

1.42.0-1,  1.42.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1, 

1.42.0-1,  1.42.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.1-0,  1.18.0-0,  1.16.0-0,  1.14.1-0,  1.14.0-0,  1.12.2-0,  1.10.0-0,  1.8.4-0,  1.6.3-1,  1.6.3-0,  1.6.1-0,  1.6.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0a0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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-genomicalignments

and update with::

   mamba update bioconductor-genomicalignments

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicalignments

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-genomicalignments:<tag>

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

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