recipe hmftools-chord

Predict HRD using somatic mutations contexts

Homepage:

https://github.com/hartwigmedical/hmftools/blob/master/chord/

License:

GPL3 / GPL-3.0-only

Recipe:

/hmftools-chord/meta.yaml

package hmftools-chord

versions:

2.1.0_beta-0

depends bioconductor-bsgenome:

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

depends bioconductor-bsgenome.hsapiens.ucsc.hg38:

depends openjdk:

>=8

depends r-base:

>=4.3,<4.4.0a0

depends r-randomforest:

depends r-stringr:

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-chord

and update with::

   mamba update hmftools-chord

To create a new environment, run:

mamba create --name myenvname hmftools-chord

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-chord:<tag>

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

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Link to this page

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