Package Recipe 'wepp'

recipe wepp

Wastewater-Based Epidemiology using Phylogenetic Placements

Homepage:: https://github.com/TurakhiaLab/WEPP
Documentation:: https://turakhia.ucsd.edu/WEPP
License:: MIT / MIT
Recipe:: /wepp/meta.yaml

WEPP (Wastewater-Based Epidemiology using Phylogenetic Placements) is a pathogen-agnostic pipeline that enhances wastewater surveillance by leveraging the pathogen's full phylogeny. It reports haplotype and lineage abundances, maps reads parsimoniously to selected haplotypes, and flags Unaccounted Alleles — those observed in the sample but unexplained by selected haplotypes, potentially indicating novel variants. WEPP performs parsimonious read placement on the mutation-annotated tree (MAT) to select a subset of haplotypes and adds their neighbors to form an initial candidate pool, which is passed to a deconvolution algorithm to estimate their relative abundances. An interactive dashboard enables visualization of haplotypes in the global phylogenetic tree and read-level analysis.

package wepp¶

Versions:

0.1.5.3-0, 0.1.5.2-0, 0.1.5.1-0, 0.1.5-0, 0.1.4.1-0

Depends:

on aiohttp
on altair
on biopython
on boost 1.78.*
on conda >=24.7.1
on jsoncpp >=1.9.6,<1.9.7.0a0
on libgcc >=14
on libstdcxx >=14
on mpich >=4.3.1,<5.0a0
on nodejs >=16,<24
on pandas
on pip
on protobuf <4
on python >=3.11,<3.12.0a0
on snakemake-minimal >=9.0
on tbb >=2021.0,<2022.0
on tbb >=2021.13.0

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 wepp

to add into an existing workspace instead, run:

pixi add wepp

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 wepp

Alternatively, to install into a new environment, run:

conda create -n envname wepp

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/wepp:<tag>

(see wepp/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/wepp/README.html)