recipe hmftools-protect

PROTECT determines the clinical evidence applicable for a particular tumor sample based on all genomic events and signatures that are determined by the Hartwig pipeline.

Homepage:

https://github.com/hartwigmedical/hmftools/blob/master/protect/README.md

License:

GPL3 / GNU General Public v3 (GPLv3)

Recipe:

/hmftools-protect/meta.yaml

package hmftools-protect

(downloads) docker_hmftools-protect

versions:

2.3-0

depends openjdk:

>=8

depends zlib:

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-protect

and update with::

   mamba update hmftools-protect

To create a new environment, run:

mamba create --name myenvname hmftools-protect

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-protect:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hmftools-protect/README.html)