recipe freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

Homepage:

https://github.com/freebayes/freebayes

Documentation:

https://github.com/freebayes/freebayes/blob/v1.3.8/README.md

License:

MIT / MIT

Recipe:

/freebayes/meta.yaml

Links:

biotools: freebayes, usegalaxy-eu: freebayes, doi: 10.48550/arXiv.1207.3907

package freebayes

(downloads) docker_freebayes

versions:
1.3.8-2,  1.3.8-1,  1.3.8-0,  1.3.7-2,  1.3.7-1,  1.3.7-0,  1.3.6-7,  1.3.6-6,  1.3.6-5, 

1.3.8-2,  1.3.8-1,  1.3.8-0,  1.3.7-2,  1.3.7-1,  1.3.7-0,  1.3.6-7,  1.3.6-6,  1.3.6-5,  1.3.6-4,  1.3.6-3,  1.3.6-2,  1.3.6-1,  1.3.6-0,  1.3.5-4,  1.3.5-3,  1.3.5-2,  1.3.5-1,  1.3.5-0,  1.3.4-0,  1.3.2-2,  1.3.2-1,  1.3.2-0,  1.3.1-0,  1.2.0-4,  1.2.0-3,  1.2.0-2,  1.2.0-0,  1.1.0.46-5,  1.1.0.46-4,  1.1.0.46-3,  1.1.0.46-2,  1.1.0.46-1,  1.1.0.46-0,  1.1.0-3,  1.1.0-2,  1.1.0-1,  1.1.0-0,  1.0.2.29-2,  1.0.2.29-1,  1.0.2.29-0,  1.0.2-0,  1.0.1-0,  0.9.21.26-0,  0.9.21.7-0

depends bzip2:

>=1.0.8,<2.0a0

depends htslib:

>=1.20,<1.22.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends parallel:

depends samtools:

depends tabixpp:

>=1.1.2,<1.1.3.0a0

depends vcflib:

>=1.0.10,<2.0a0

depends wfa2-lib:

>=2.3.5,<3.0a0

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 freebayes

and update with::

   mamba update freebayes

To create a new environment, run:

mamba create --name myenvname freebayes

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/freebayes:<tag>

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

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Link to this page

Render an install-with-bioconda 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/freebayes/README.html)