Tutorials

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Running Tutorials on Your Computer

We have created a debian repository to make it easier to use our tutorials. Using this repository will require that you have administrator access to the computer on which you'll be using them. If you don't have this level of access, we also provide a pre-configured virtual machine image that will allow you to install software as root.

The VM Image is available here. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.

If you would like to use our repository on a VM or on your computer, follow these configuration steps. Please run as the root user or using the sudo command.

sudo add-apt-repository ppa:webupd8team/java
sudo echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" > /etc/apt/sources.list.d/statgen.list
sudo apt-get update

GWAS: Data Quality Control

Installing Packages

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

sudo apt-get install plink-tutorial

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


GWAS: Association Analysis Controlling for Population Substructure

Installing Packages

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

sudo apt-get install plink-tutorial

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


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.

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.

Variant Association Tools

Installing Packages

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

sudo apt-get install vtools-tutorial

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