recipe flippyr

This package is designed to align a PLINK fileset with a FASTA reference genome.

Homepage:

https://github.com/BEFH/flippyr

License:

MIT / MIT

Recipe:

/flippyr/meta.yaml

Flippy is a simple, fast script to ensure that PLINK filesets are aligned to a reference genome in FASTA format. It identifies and fixes strand flipping, and reversed alleles. It removes ambiguous (palindromic) alleles and sites that do not match the reference genome. It also recognizes and removes multi- allelic sites and indels by default. Instructions and more details can be found on GitHub.

package flippyr

(downloads) docker_flippyr

versions:

0.6.1-0,  0.6.0-0,  0.5.3-0,  0.4.0-0

depends pandas:

depends pyfaidx:

depends python:

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 flippyr

and update with::

   mamba update flippyr

To create a new environment, run:

mamba create --name myenvname flippyr

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/flippyr:<tag>

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

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Link to this page

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