Difference between revisions of "Tutorials"

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If you want to install all below exercises, you could use the following command. In addition, you could also install these exercise separately using specific commands listed in each section below.
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If you want to install all below exercises, you could use the following command. In addition, you could also install specific exercise at your demands using commands listed in each section below.
  
 
<pre>the command to install all  
 
<pre>the command to install all  

Revision as of 13:45, 6 June 2018

Running Tutorials on Your Computer

We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to the computer with Linux System. If you don't have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as VULTR. Second, you can install a Virtual Machine program (such as VirtualBox) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine.

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

To install the repository on the cloud server, virtual machine, or your own computer, you need to follow these configuration steps. Please run as the root user or using the sudo command.

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

If you want to install all below exercises, you could use the following command. In addition, you could also install specific exercise at your demands using commands listed in each section below.

the command to install all 


Annotation

Functional Annotation Exercise [PDF]

Cochran Armitage Trend Test

GATK and IGV

Software Links

Result Files

GenABEL

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.

Regression

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.

Population Genetics

PSEQ

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.