recipe pybdei

Maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters from phylogenetic trees.

Homepage:

https://github.com/evolbioinfo/bdei

License:

GPL2 / LGPL-2.1

Recipe:

/pybdei/meta.yaml

Links:

doi: 10.1093/sysbio/syad059

PyBDEI provides tools for fast and accurate maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters from phylogenetic trees.

package pybdei

versions:

0.13-0

depends ete3:

>=3.1.3

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends nlopt:

>=2.7.1,<2.8.0a0

depends numpy:

>=1.19,<3

depends numpy:

>=1.24.0

depends python:

>=3.12,<3.13.0a0

depends python_abi:

3.12.* *_cp312

depends scipy:

>=1.11.1

depends six:

>=1.16.0

depends treesimulator:

>=0.1.22

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 pybdei

and update with::

   mamba update pybdei

To create a new environment, run:

mamba create --name myenvname pybdei

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/pybdei:<tag>

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

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