recipe phu

Phage Utilities (phu): modular toolkit for clustering, classifying, and analyzing viral sequences.

Homepage:

https://github.com/camilogarciabotero/phu

Documentation:

https://camilogarciabotero.github.io/phu

License:

MIT / MIT

Recipe:

/phu/meta.yaml

**phu** (Phage Utilities) is a Python toolkit designed for viral bioinformatics workflows. It provides modular commands to handle tasks such as:

* `seqclust`: dereplication and clustering of viral contigs into vOTUs and putative species-level groups. * `taxasimplify`: simplification and parsing of viral taxonomy assignments.

package phu

versions:

0.4.0-0,  0.3.0-0,  0.2.1-0,  0.1.1-0

depends mypy:

depends pandas:

depends pyrodigal:

depends pytest:

depends python:

>=3.10

depends ruff:

depends seqkit:

depends typer:

depends vclust:

requirements:

additional platforms:

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 phu

and update with::

   mamba update phu

To create a new environment, run:

mamba create --name myenvname phu

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/phu:<tag>

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

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