Package Recipe 'wasp2'

recipe wasp2

Allele-specific analysis of next-generation sequencing data with Rust acceleration

Homepage:: https://github.com/mcvickerlab/WASP2
Documentation:: https://mcvickerlab.github.io/WASP2/
License:: MIT / MIT
Recipe:: /wasp2/meta.yaml
Links:: biotools: wasp2

WASP2 is a high-performance tool for allele-specific analysis of NGS data. It provides functionality for variant counting, read remapping for bias correction, and statistical analysis of allelic imbalance. The package includes a Rust extension for accelerated BAM processing.

package wasp2¶

Versions:

1.4.0-0

Depends:

on anndata >=0.8.0,<0.12.0
on bcftools
on bedtools
on bzip2 >=1.0.8,<2.0a0
on htslib >=1.23,<1.24.0a0
on libcurl >=8.18.0,<9.0a0
on libcxx >=19
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on numpy >=1.21.0
on pandas >=1.5.0,<3.0.0
on polars >=0.19.0
on pybedtools >=0.9.0
on pysam >=0.21.0
on python >=3.11,<3.12.0a0
on python_abi 3.11.* *_cp311
on rich >=13.0.0
on samtools >=1.10
on scanpy >=1.9.0
on scipy >=1.10.0
on typer >=0.12.0

Additional platforms:

linux-aarch64, osx-arm64

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 wasp2

to add into an existing workspace instead, run:

pixi add wasp2

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 wasp2

Alternatively, to install into a new environment, run:

conda create -n envname wasp2

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/wasp2:<tag>

(see wasp2/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/wasp2/README.html)