recipe arriba

Fast and accurate gene fusion detection from RNA-Seq data

Homepage:

https://github.com/suhrig/arriba

License:

MIT

Recipe:

/arriba/meta.yaml

package arriba

versions:

2.4.0-4,  2.4.0-3,  2.4.0-2,  2.4.0-1,  2.4.0-0,  2.3.0-1,  2.3.0-0,  2.2.1-2,  2.2.1-1, 

2.4.0-4,  2.4.0-3,  2.4.0-2,  2.4.0-1,  2.4.0-0,  2.3.0-1,  2.3.0-0,  2.2.1-2,  2.2.1-1,  2.2.1-0,  2.2.0-0,  2.1.0-2,  2.1.0-1,  2.1.0-0,  2.0.0-1,  2.0.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.1-0

depends bioconductor-genomicalignments:

depends bioconductor-genomicranges:

depends htslib:

>=1.20,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-base:

>=3.3.0

depends r-circlize:

depends samtools:

>=1.9

depends star:

>=2.7.11b

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 arriba

and update with::

   mamba update arriba

To create a new environment, run:

mamba create --name myenvname arriba

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/arriba:<tag>

(see `arriba/tags`_ for valid values for ``<tag>``)

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