Tutorials

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Running Tutorials on Your Computer

Starting Fall 2019 we adopt docker to run our course material . We have created various docker repositories with source material freely available from github for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) for your own data analysis.

In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands.

Pre-requisites

Software you need to install on your computer are SoS (a workflow system to run our course utility script) and docker.

Mac and Linux users

SoS requires Python 3.6+ to run. It is recommended that you install Miniconda to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type pip install sos to install SoS, or, check out here for alternative installation methods if you have troubles with that command. To install docker from command line please follow our instructions here. Alternatively Mac users can download docker app for Mac and install from a graphical interface.

Finally please download our utility script src/statgen-setup to your PATH and change it to executable, eg, chmod +x ~/bin/statgen-setup if you put it under ~/bin which is part of your PATH. To verify your setup, type: 

statgen-setup -h

you should see some meaningful output.

Windows users

Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows.

Tutorial specific instructions

Material and instructions for specific exercise are listed in each section below (only those using statgen-setup command are relevant to our docker based tutorials). They provide links to materials and a minimal set of commands to use for launching and running an exercise. For advanced options and other features provided by our utility script please read here our complete documentation to the utility script.

Alohomora

Annotation

To run the exercise from docker image provided, 

statgen-setup login --tutorial annovar

The "statgen-setup" script is available here and can be installed following these instructions.

Annovar MEndelian

Cochran Armitage Trend Test


Epistasis (PLINK and CASSI)

To run the exercise from docker image provided, 

statgen-setup login --tutorial epistasis

The "statgen-setup" script is available here and can be installed following these instructions.


FastLMM

To run the exercise from docker image provided, 

statgen-setup login --tutorial fastlmm-gcta

The "statgen-setup" script is available here and can be installed following these instructions.

GCTA

To run the exercise from docker image provided, 

statgen-setup login --tutorial fastlmm-gcta

The "statgen-setup" script is available here and can be installed following these instructions.

Gemini

To run the exercise from docker image provided, 

statgen-setup login --tutorial gemini

The "statgen-setup" script is available here and can be installed following these instructions.


Genehunter


To install from packages, follow the configuration steps above and run the following command. 

sudo apt-get install genehunter-tutorial

The exercise's files will then be installed in the folder /home/shared/genehunter. You can run from there or copy the files into your user's home directory and proceed with the exercise.

GWAS: Data Quality Control

To run the exercise from docker image provided, 

statgen-setup login --tutorial plink

The "statgen-setup" script is available here and can be installed following these instructions.


GWAS: Association Analysis Controlling for Population Substructure

To run the exercise from docker image provided, 

statgen-setup login --tutorial plink

The "statgen-setup" script is available here and can be installed following these instructions.


Homozygosity Mapper

IGV

To run the exercise from docker image provided, 

statgen-setup login --tutorial igv

The "statgen-setup" script is available here and can be installed following these instructions.

Linkage/FastLinkage


To run the exercise from docker image provided, 

statgen-setup login --tutorial mlink

The "statgen-setup" script is available here and can be installed following these instructions.

Pleiotropy

To run the exercise from docker image provided, 

statgen-setup login --tutorial pleiotropy

The "statgen-setup" script is available here and can be installed following these instructions.

Polygenic risk prediction (NPS method)

To run the exercise from docker image provided, 

statgen-setup login --tutorial nps

The "statgen-setup" script is available here and can be installed following these instructions.

Population Genetics


To run the exercise from docker image provided, 

statgen-setup login --tutorial popgen

The "statgen-setup" script is available here and can be installed following these instructions.

PSEQ

To run the exercise from docker image provided, 

statgen-setup login --tutorial pseq

The "statgen-setup" script is available here and can be installed following these instructions.

Regression

To run the exercise from docker image provided, 

statgen-setup login --tutorial regression

The "statgen-setup" script is available here and can be installed following these instructions.

RV-TDT

Installing Packages

To install from packages, follow the configuration steps above and run the following command. 

sudo apt-get install rvtdt-tutorial

The exercise's files will then be installed in the folder /home/shared/rvtdt. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SEQLinkage


To install from packages, follow the configuration steps above and run the following command. 

sudo apt-get install seqlinkage-tutorial

The exercise's files will then be installed in the folder /home/shared/seqlinkage. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SEQSpark

Installing Packages

To install from packages, follow the configuration steps above and run the following command. 

sudo apt-get install seqspark-tutorial

The exercise's files will then be installed in the folder /home/shared/seqspark. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.

SLINK

To run the exercise from docker image provided, 

statgen-setup login --tutorial slink

The "statgen-setup" script is available here and can be installed following these instructions.


SUPERLINK

Variant Association Tools


To run the exercise from docker image provided, 

statgen-setup login --tutorial vat

The "statgen-setup" script is available here and can be installed following these instructions.

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