recipe hmftools-cuppa

Predict tissue of origin for tumor samples from WGTS data.

Homepage:

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

License:

GPL3 / GPL-3.0-only

Recipe:

/hmftools-cuppa/meta.yaml

package hmftools-cuppa

versions:

2.3.0_beta-1,  2.3.0_beta-0,  2.2.1-0,  2.1.1-0,  1.8.1-0

depends numpy:

>=1.24

depends openjdk:

>=8

depends pandas:

2.0.*

depends python:

3.11

depends r-base:

>=4.2,<4.3.0a0

depends r-ggh4x:

>=0.2

depends r-ggplot2:

>=3.5

depends r-patchwork:

>=1.2

depends r-stringr:

>=1.5

depends scikit-learn:

1.3.0

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-cuppa

and update with::

   mamba update hmftools-cuppa

To create a new environment, run:

mamba create --name myenvname hmftools-cuppa

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-cuppa:<tag>

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

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