Difference between revisions of "Tutorials"

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(→‎Running Tutorials on Your Computer)
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* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
 
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
 
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
 
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
−
 
  
  
 
===Tutorial specific instructions===
 
===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.
 
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.
 +
 +
We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.
  
 
==Alohomora==
 
==Alohomora==
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==Annotation==
 
==Annotation==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
  
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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].
 
  
 
==Annovar MEndelian==
 
==Annovar MEndelian==
 
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
−
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
+
* [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
−
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
+
* [https://statgen.us/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
  
 
==Cochran Armitage Trend Test==
 
==Cochran Armitage Trend Test==
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<pre>statgen-setup login --tutorial epistasis
 
<pre>statgen-setup login --tutorial epistasis
 
</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].
 
  
  
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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].
 
  
 
==GCTA==
 
==GCTA==
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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].
 
  
 
==Gemini==
 
==Gemini==
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<pre>statgen-setup login --tutorial gemini
 
<pre>statgen-setup login --tutorial gemini
 
</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].
 
−
 
  
  
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<pre>statgen-setup login --tutorial plink
 
<pre>statgen-setup login --tutorial plink
 
</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].
 
−
 
  
  
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<pre>statgen-setup login --tutorial plink
 
<pre>statgen-setup login --tutorial plink
 
</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].
 
−
 
  
  
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* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
 
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
  
−
To run the exercise from docker image provided,
 
−
 
−
<pre>statgen-setup login --tutorial igv
 
−
</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].
 
  
 
==Linkage/FastLinkage==
 
==Linkage/FastLinkage==
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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].
 
  
 
==Pleiotropy==
 
==Pleiotropy==
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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].
 
  
 
==Polygenic risk prediction (NPS method)==
 
==Polygenic risk prediction (NPS method)==
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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].
+
 
 +
==Polygenic risk prediction (LDpred2 method)==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]
 +
 
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup launch --tutorial ldpred2
 +
</pre>
 +
 
 +
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
 +
 
 +
<pre>get-data</pre>
 +
 
 +
to load the data-set to the JupyterLab workspace.
 +
 
  
 
<!--
 
<!--
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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].
 
  
 
==PSEQ==
 
==PSEQ==
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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].
+
 
 +
==REGENIE==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]
 +
 
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup launch --tutorial regenie
 +
</pre>
 +
 
 +
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
 +
 
 +
<pre>get-data</pre>
 +
 
 +
to load the data-set to the JupyterLab workspace.
 +
 
  
 
==Regression==
 
==Regression==
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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].
 
  
 
==RV-TDT==
 
==RV-TDT==
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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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==Variant Association Tools==
 
==Variant Association Tools==
−
* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
−
* [[VAT Commands in Exercise|Exercise Commands]]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
  
  
 
To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
−
<pre>statgen-setup login --tutorial vat
+
<pre>statgen-setup launch --tutorial vat
 
</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].
 

Revision as of 02:41, 4 November 2021

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) or even a high performance computing cluster (if properly configured) for your own data analysis.



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.

We use a script "statgen-setup" to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.

Alohomora

Annotation

To run the exercise from docker image provided, 

statgen-setup login --tutorial annovar


Annovar MEndelian

Cochran Armitage Trend Test


Epistasis (PLINK and CASSI)

To run the exercise from docker image provided, 

statgen-setup login --tutorial epistasis


FastLMM

To run the exercise from docker image provided, 

statgen-setup login --tutorial fastlmm-gcta


GCTA

To run the exercise from docker image provided, 

statgen-setup login --tutorial fastlmm-gcta


Gemini

To run the exercise from docker image provided, 

statgen-setup login --tutorial gemini


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


GWAS: Association Analysis Controlling for Population Substructure

To run the exercise from docker image provided, 

statgen-setup login --tutorial plink


Homozygosity Mapper

IGV


Linkage/FastLinkage


To run the exercise from docker image provided, 

statgen-setup login --tutorial mlink


Pleiotropy

To run the exercise from docker image provided, 

statgen-setup login --tutorial pleiotropy


Polygenic risk prediction (NPS method)

To run the exercise from docker image provided, 

statgen-setup login --tutorial nps


Polygenic risk prediction (LDpred2 method)


To run the exercise from docker image provided, 

statgen-setup launch --tutorial ldpred2

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type 

get-data

to load the data-set to the JupyterLab workspace.


Population Genetics


To run the exercise from docker image provided, 

statgen-setup login --tutorial popgen


PSEQ

To run the exercise from docker image provided, 

statgen-setup login --tutorial pseq


REGENIE


To run the exercise from docker image provided, 

statgen-setup launch --tutorial regenie

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type 

get-data

to load the data-set to the JupyterLab workspace.


Regression

To run the exercise from docker image provided, 

statgen-setup login --tutorial 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.

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 launch --tutorial vat
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