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 boost-cpp:

depends bzip2:

>=1.0.8,<2.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libcurl:

>=8.12.1,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends liblzma:

>=5.6.4,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

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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