recipe bioconductor-rhisat2

R Wrapper for HISAT2 Aligner

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Rhisat2.html

License:

GPL-3

Recipe:

/bioconductor-rhisat2/meta.yaml

An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

package bioconductor-rhisat2

versions:

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.3-0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-sgseq:

>=1.40.0,<1.41.0

depends bioconductor-sgseq:

>=1.40.0,<1.41.0a0

depends bioconductor-txdbmaker:

>=1.2.0,<1.3.0

depends bioconductor-txdbmaker:

>=1.2.0,<1.3.0a0

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:

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-rhisat2

and update with::

   mamba update bioconductor-rhisat2

To create a new environment, run:

mamba create --name myenvname bioconductor-rhisat2

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-rhisat2:<tag>

(see `bioconductor-rhisat2/tags`_ for valid values for ``<tag>``)

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