Package Recipe 'shapeit5'

recipe shapeit5

Fast and accurate method for estimation of haplotypes (phasing).

Homepage:: https://odelaneau.github.io/shapeit5
Developer docs:: https://github.com/odelaneau/shapeit5
License:: MIT / MIT
Recipe:: /shapeit5/meta.yaml
Links:: doi: 10.1101/2022.10.19.512867, biotools: shapeit5

This package provides the software SHAPEIT5. SHAPEIT5 estimates haplotypes in large datasets (WGS, WES, SNP array), with a special focus on rare variants.

package shapeit5¶

Versions:

5.1.1-2, 5.1.1-0, 1.0.0-0

Depends:

on boost-cpp
on bzip2 >=1.0.8,<2.0a0
on htslib >=1.21,<1.24.0a0
on libcurl >=8.12.1,<9.0a0
on libdeflate >=1.22,<1.23.0a0
on libgcc >=13
on liblzma >=5.6.4,<6.0a0
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0

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 shapeit5

to add into an existing workspace instead, run:

pixi add shapeit5

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 shapeit5

Alternatively, to install into a new environment, run:

conda create -n envname shapeit5

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/shapeit5:<tag>

(see shapeit5/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/shapeit5/README.html)