recipe unifrac

Fast phylogenetic diversity calculations.

Homepage:

https://github.com/biocore/unifrac

Documentation:

https://github.com/biocore/unifrac/blob/1.5/README.md

License:

BSD / BSD-3-Clause

Recipe:

/unifrac/meta.yaml

Links:

doi: 10.1038/s41592-018-0187-8, doi: 10.1128/msystems.00028-22

UniFrac is a commonly phylogenetic diversity distance metric used in microbiome research. The metric relates two microbiome samples together within the context of an evolutionary history, and produces a distance that corresponds to how similar two samples by the amount of overlapping branch length.

package unifrac

versions:

1.5-0,  1.3.2-0,  1.3-0,  1.2-0,  1.1.1-1,  1.1.1-0,  1.1.0-0,  1.0.0-1,  1.0.0-0, 

1.5-0,  1.3.2-0,  1.3-0,  1.2-0,  1.1.1-1,  1.1.1-0,  1.1.0-0,  1.0.0-1,  1.0.0-0,  0.20.3-0,  0.20.2-1,  0.20.2-0,  0.20.1-0,  0.20.0-1,  0.20.0-0,  0.10.0-1,  0.10.0-0,  0.9.3-1,  0.9.3-0

depends biom-format:

depends h5py:

>=3.3.0

depends iow:

>=1.0.8,<2.0a0

depends libgcc:

>=13

depends numpy:

>=1.21,<3

depends numpy:

>=2.2.5,<3.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends scikit-bio:

>=0.6.0

depends scipy:

>=1.9.0

depends unifrac-binaries:

>=1.5

depends unifrac-binaries:

>=1.5,<2.0a0

requirements:

additional platforms:

osx-arm64

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 unifrac

and update with::

   mamba update unifrac

To create a new environment, run:

mamba create --name myenvname unifrac

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/unifrac:<tag>

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

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