gelog/plink repository overview

⁠PLINK

⁠

⁠Supported tags and respective Dockerfile links

• 1.07-bin, latest (plink-1.07-bin/docker/Dockerfile)⁠ based on Ubuntu:14.04.2⁠ image.

⁠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?

• Plink v1: Project page⁠ and Source code (zip file)⁠
• Plink v2: Project page⁠ and Source code (Git repo)⁠

⁠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)