recipe ba3

Bayesian inference of recent migration rates from multilocus genotypes

Homepage:

https://github.com/brannala/BA3

Documentation:

https://github.com/brannala/BA3/wiki

License:

AGPL / AGPL-3.0-or-later

Recipe:

/ba3/meta.yaml

BA3 (BayesAss Edition 3) is a Bayesian MCMC program that estimates recent migration rates between populations from multilocus genotype data (SNPs or microsatellites). In addition to migration rates, it infers first- and second-generation migrant individuals, population allele frequencies, and inbreeding coefficients. Supports both the native BA3 text format and VCF input.

package ba3

Versions:

3.4.4-0

Depends:

• on __osx >=10.13

• on gsl >=2.7,<2.8.0a0

• on htslib >=1.23.1,<1.24.0a0

• on libcxx >=19

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install ba3

to add into an existing workspace instead, run:

pixi add ba3

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install ba3

Alternatively, to install into a new environment, run:

conda create -n envname ba3

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/ba3:<tag>

(see ba3/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/ba3/README.html)