recipe bioconductor-seqarray

Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Homepage:

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

License:

GPL-3.0-only

Recipe:

/bioconductor-seqarray/meta.yaml

Links:

biotools: seqarray

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

package bioconductor-seqarray

versions:

1.46.0-0,  1.42.4-1,  1.42.0-0,  1.40.1-0,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0, 

1.46.0-0,  1.42.4-1,  1.42.0-0,  1.40.1-0,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.2-0,  1.22.2-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends bioconductor-gdsfmt:

>=1.42.0,<1.43.0

depends bioconductor-gdsfmt:

>=1.42.0,<1.43.0a0

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-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

linux-aarch64

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-seqarray

and update with::

   mamba update bioconductor-seqarray

To create a new environment, run:

mamba create --name myenvname bioconductor-seqarray

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-seqarray:<tag>

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

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