recipe mrbayes_volpiano

Bayesian Inference of Phylogeny (Volpiano edition)

Homepage:

https://github.com/gaballench/mrbayes_volpiano

License:

GPL3 / GPL-3.0-or-later

Recipe:

/mrbayes_volpiano/meta.yaml

Links:

biotools: mrbayes_volpiano

This is a fork of MrBayes v3.2.7a, a programme for estimation of phylogenetic trees using Bayesian inference. This fork differs from the original in that the standard character coding is no longer intended for morphology in biological datasets but rather for the encoding of plainchant melodies in the volpiano format. The original README is provided below as well as the license and modified source code. A note has been added to the greeting text to make it clear that this is a fork only intended to be used for analysing plainchant melodies in volpiano format rather than the original biological sequence data.

package mrbayes_volpiano

(downloads) docker_mrbayes_volpiano

Versions:

3.2.7a-0

Depends:

  • on beagle-lib <4

  • on beagle-lib >=3.1.2,<4.0a0

  • on libgcc >=13

  • on ncurses >=6.5,<7.0a0

  • on openmpi >=4.1.6,<5.0a0

  • on readline >=8.2,<9.0a0

Additional platforms:
linux-aarch64,  osx-arm64

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 mrbayes_volpiano

to add into an existing workspace instead, run:

pixi add mrbayes_volpiano

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 mrbayes_volpiano

Alternatively, to install into a new environment, run:

conda create -n envname mrbayes_volpiano

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/mrbayes_volpiano:<tag>

(see mrbayes_volpiano/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.

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Render an install-with-bioconda badge with the following MarkDown:

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