Difference between revisions of "Tutorials"

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==Running Tutorials on Your Computer==
 
==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 a 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 [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ VirtualBox]) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine. You can refer to these online videos [[VirtualBox Installation|here]] to install VirtualBox on your computer.
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We have adopted [https://www.docker.com/ docker] to run our course material since Fall 2019. We have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with source material freely available from [https://github.com/statgenetics/statgen-courses 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 section we will discuss how to set it up and run course materials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands.
  
The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova here]. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
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===Pre-requisites===
  
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.
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Software you need to install on your computer are <code>SoS</code> (a workflow system to run our course utility script) and <code>docker</code>.
  
<pre>echo "deb [trusted=yes] https://statgen.us/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
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====Mac and Linux users====
sudo add-apt-repository -y ppa:webupd8team/java
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sudo apt-get update
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<code>SoS</code> requires Python 3.6+ to run. It is recommended that you install [https://docs.conda.io/en/latest/miniconda.html Miniconda] to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type <code>pip install sos</code> to install <code>SoS</code>, or, check out [https://vatlab.github.io/sos-docs/running.html here for alternative installation methods] if you have troubles with that command.
</pre>
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To install <code>docker</code> please follow our instruction [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here].
 +
 
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Additionally please download our utility script [https://raw.githubusercontent.com/statgenetics/statgen-courses/master/src/statgen-setup <code>src/statgen-setup</code>] to your <code>PATH</code> and change it to executable, eg, <code>chmod +x ~/bin/statgen-setup</code> if you put it under <code>~/bin</code> which is part of your <code>PATH</code>. To verify your setup, type:
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<pre>statgen-setup -h</pre>
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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.
  
We have made a video tutorial to show you how to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
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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'').
  
 
==Alohomora==
 
==Alohomora==
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
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<pre>statgen-setup login --tutorial annovar
statgen-setup login --tutorial annovar
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial gemini
statgen-setup login --tutorial gemini
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</pre>
 
</pre>
  
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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.
 
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.
  
==Homozygosity Mapper==  
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==Homozygosity Mapper==
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
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*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
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* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
*[http://www.homozygositymapper.org Data Sets]
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* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
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* [http://www.homozygositymapper.org Data Sets]
  
 
==IGV==
 
==IGV==
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
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<pre>statgen-setup login --tutorial igv
statgen-setup login --tutorial igv
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial mlink
statgen-setup login --tutorial mlink
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial popgen
statgen-setup login --tutorial popgen
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
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<pre>statgen-setup login --tutorial pseq
statgen-setup login --tutorial pseq
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial regression
statgen-setup login --tutorial regression
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</pre>
 
</pre>
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial slink
statgen-setup login --tutorial slink
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</pre>
 
</pre>
  
 
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
 
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
 +
  
  
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To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial vat
statgen-setup login --tutorial vat
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</pre>
 
</pre>
  

Revision as of 02:51, 22 February 2020

Running Tutorials on Your Computer

We have adopted docker to run our course material since Fall 2019. 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 section we will discuss how to set it up and run course materials 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 please follow our instruction here.

Additionally 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.

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).

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

GATK and IGV

Software Links

Result Files

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.

GenABEL

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

sudo apt-get install genabel-tutorial

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

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

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.

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.

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.

VAT Mendelian


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

sudo apt-get install vtools-mendelian-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.