recipe eagle2

The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.

Homepage:

https://github.com/poruloh/Eagle

License:

GPL-3.0-or-later

Recipe:

/eagle2/meta.yaml

Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas; a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option. (The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without a reference and also supports phasing chrX.

package eagle2

versions:

2.4.1-0

depends boost-cpp:

>=1.85.0,<2.0a0

depends bzip2:

>=1.0.8,<2.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends openblas:

>=0.3.28,<1.0a0

depends zlib:

>=1.2.13,<2.0a0

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 eagle2

and update with::

   mamba update eagle2

To create a new environment, run:

mamba create --name myenvname eagle2

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/eagle2:<tag>

(see `eagle2/tags`_ for valid values for ``<tag>``)

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