recipe varscan

variant detection in massively parallel sequencing data

Homepage:

http://dkoboldt.github.io/varscan/

License:

The Non-Profit Open Software License version 3.0 (NPOSL-3.0)

Recipe:

/varscan/meta.yaml

Links:

biotools: varscan

package varscan

(downloads) docker_varscan

versions:
2.4.6-0,  2.4.4-1,  2.4.4-0,  2.4.3-2,  2.4.3-1,  2.4.3-0,  2.4.2-2,  2.4.2-1,  2.4.2-0, 

2.4.6-0,  2.4.4-1,  2.4.4-0,  2.4.3-2,  2.4.3-1,  2.4.3-0,  2.4.2-2,  2.4.2-1,  2.4.2-0,  2.4.1-0,  2.4.0-1,  2.4.0-0,  2.3.7-4,  2.3.7-3,  2.3.7-2,  2.3.7-0

depends openjdk:

depends zlib:

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 varscan

and update with::

   mamba update varscan

To create a new environment, run:

mamba create --name myenvname varscan

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/varscan:<tag>

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

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