recipe hmftools-gripss

GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output to produce a high confidence set of somatic SV for a tumor sample.

Homepage:

https://github.com/hartwigmedical/hmftools/tree/master/gripss

License:

GPL / GPL-3.0-only

Recipe:

/hmftools-gripss/meta.yaml

package hmftools-gripss

versions:

2.4-0,  2.3.5-0,  2.3.2-0,  2.2-0,  2.1-0,  2.0-0,  1.11-0,  1.9-1,  1.9-0, 

2.4-0,  2.3.5-0,  2.3.2-0,  2.2-0,  2.1-0,  2.0-0,  1.11-0,  1.9-1,  1.9-0,  1.8-0,  1.7-0,  1.6-0,  1.5-0,  1.4-0,  1.3-0,  1.2-0,  1.1-0,  1.0-0

depends openjdk:

>=8

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 hmftools-gripss

and update with::

   mamba update hmftools-gripss

To create a new environment, run:

mamba create --name myenvname hmftools-gripss

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/hmftools-gripss:<tag>

(see `hmftools-gripss/tags`_ for valid values for ``<tag>``)

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