recipe shapeit5

Fast and accurate method for estimation of haplotypes (phasing)

Homepage:

https://odelaneau.github.io/shapeit5/

License:

MIT

Recipe:

/shapeit5/meta.yaml

Links:

doi: 10.1101/2022.10.19.512867

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:

5.1.1-0,  1.0.0-0

depends boost-cpp:

>=1.74.0,<1.74.1.0a0

depends bzip2:

>=1.0.8,<2.0a0

depends htslib:

>=1.17,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

requirements:

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 shapeit5

and update with::

   mamba update shapeit5

To create a new environment, run:

mamba create --name myenvname shapeit5

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/shapeit5:<tag>

(see `shapeit5/tags`_ for valid values for ``<tag>``)

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