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

(downloads) docker_eagle2

Versions:

2.4.1-0

Depends:

  • on boost-cpp >=1.85.0,<2.0a0

  • on bzip2 >=1.0.8,<2.0a0

  • on htslib >=1.21,<1.24.0a0

  • on libgcc >=12

  • on libstdcxx >=12

  • on libzlib >=1.2.13,<2.0a0

  • on openblas >=0.3.28,<1.0a0

  • on zlib >=1.2.13,<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 eagle2

to add into an existing workspace instead, run:

pixi add eagle2

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 eagle2

Alternatively, to install into a new environment, run:

conda create -n envname eagle2

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/eagle2:<tag>

(see eagle2/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.

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