recipe pyclone

PyClone: A probabilistic model for inferring clonal population structure from deep NGS sequencing.

Homepage:

https://github.com/Roth-Lab/pyclone/

License:

custom

Recipe:

/pyclone/meta.yaml

Links:

doi: 10.1038/nmeth.2883

PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.

package pyclone

versions:

0.13.1-0

depends matplotlib-base:

depends numba:

depends numpy:

depends pandas:

depends pydp:

>=0.2.4

depends python:

<3

depends pyyaml:

depends scipy:

depends seaborn:

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 pyclone

and update with::

   mamba update pyclone

To create a new environment, run:

mamba create --name myenvname pyclone

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/pyclone:<tag>

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

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