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PLINK



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What is Plink?

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).
Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.

Why is there 2 plink versions?

  • Plink 1.07 is the latest version of plink released in 2009 by the Broad Institute.
  • Plink 2 is a complete rewrite of Plink v1, done by Christopher Chang (China). Currently in beta, the latest release is v1.90.

Is this the official repository for Plink source code?

NO. This repository holds a copy of the latest stable release of Plink v1.07.

Where can I find the official Plink?

What is the directory structure of this project?

  • plink-1.07-bin/docker/: Dockerfile for the released version of Plink v1.
  • plink-1.07-src/: A copy of Plink 1.07 source code
  • plink-2.0-bin/docker/: Dockerfile for the released version of Plink v2.

What is Docker?

Docker is an open platform for developers and sysadmins to build, ship, and run distributed applications.
Consisting of Docker Engine, a portable, lightweight runtime and packaging tool, and Docker Hub, a cloud service for sharing applications and automating workflows, Docker enables apps to be quickly assembled from components and eliminates the friction between development, QA, and production environments.
As a result, IT can ship faster and run the same app, unchanged, on laptops, data center VMs, and any cloud.

https://www.docker.com/whatisdocker/

What is a Docker Image?

Docker images are the basis of containers.
Images are read-only, while containers are writeable.
Only the containers can be executed by the operating system.

https://docs.docker.com/terms/image/

How to use this image?

To use data that is inside the container

docker run --rm -ti gelog/plink --file /usr/local/plink/test

To use data that is OUTSIDE the container, you need to use a volume (-v)

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