recipe medicc2

Whole-genome doubling-aware copy number phylogenies for cancer evolution

Homepage:

https://bitbucket.org/schwarzlab/medicc2

License:

GPL3 / GPL-3.0-or-later

Recipe:

/medicc2/meta.yaml

Links:

doi: 10.1186/s13059-022-02794-9

For more information see the accompanying biorxiv preprint "Kaufmann et al. Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2."

package medicc2

versions:

1.1.2-1,  1.1.2-0,  1.1.1-0,  1.0.4-0,  1.0.2-1,  1.0.2-0,  1.0.0-1,  1.0.0-0,  0.9.2-0, 

1.1.2-1,  1.1.2-0,  1.1.1-0,  1.0.4-0,  1.0.2-1,  1.0.2-0,  1.0.0-1,  1.0.0-0,  0.9.2-0,  0.9.1-1,  0.9.1-0,  0.8.3-0,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6b1-0,  0.5b4-0,  0.5b3-0

depends biopython:

>=1.78

depends joblib:

>=1.0.1

depends libgcc:

>=13

depends libstdcxx:

>=13

depends matplotlib-base:

>=3.3.4

depends numpy:

>=1.20.1,<2.0

depends numpy:

>=1.21,<3

depends openfst:

>=1.8.2,<1.8.3.0a0

depends pandas:

>=1.2,<2.1

depends pyranges:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends pyyaml:

>=5.4.1

depends scipy:

>=1.7

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 medicc2

and update with::

   mamba update medicc2

To create a new environment, run:

mamba create --name myenvname medicc2

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/medicc2:<tag>

(see `medicc2/tags`_ for valid values for ``<tag>``)

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