- recipe phu
Phage Utilities (phu): modular toolkit for clustering, classifying, and analyzing viral sequences.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
**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:
0.6.0-0,0.5.0-0,0.4.4-0,0.4.3-0,0.4.0-0,0.3.0-0,0.2.1-0,0.1.1-0- Depends:
on hmmer
on mypy
on pandas
on pyhmmer
on pyrodigal
on pyrodigal-gv
on pytest
on python
>=3.10on ruff
on seqkit
on typer
on vclust
- 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 phu
to add into an existing workspace instead, run:
pixi add phu
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 phu
Alternatively, to install into a new environment, run:
conda create -n envname phu
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/phu:<tag>
(see phu/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¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/phu/README.html)
