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==Running Tutorials on Your Computer==
 
==Running Tutorials on Your Computer==
Since Fall 2019 we adopted [https://www.docker.com/ docker] to run our course material . 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.  
+
Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . 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) or even a high performance computing cluster (if properly configured) 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.
+
===General instructions===
 +
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer]
 +
* [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]
  
===Pre-requisites===
 
 
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>.
 
 
====Mac and Linux users====
 
 
<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. To install <code>docker</code> from command line please follow our instructions [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface.
 
 
Finally 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:
 
 
<pre>statgen-setup -h</pre>
 
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===
 
===Tutorial specific instructions===
 +
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.
  
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 our [https://github.com/statgenetics/statgen-courses/blob/master/README.md complete documentation to the utility script here].
+
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.
  
 
==Alohomora==
 
==Alohomora==
Line 30: Line 18:
 
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
 
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
  
==Annotation==
+
==Annovar complex traits==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
  
Line 39: Line 27:
 
</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 traits==
 
+
==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==
* [http://statgen.us/files/tutorials/Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
  
==GATK and IGV==
 
* [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>]
 
  
====Software Links====
 
:* [https://www.broadinstitute.org/gatk/ GATK]
 
:* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
 
  
====Result Files====
+
==Epistasis (PLINK and CASSI)==
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Epistasis_PLINK_CASSI.pdf Epistasis exercise <nowiki>[PDF]</nowiki>]
  
==Gemini==
+
To run the exercise from docker image provided,
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
+
 
 +
<pre>statgen-setup login --tutorial epistasis
 +
</pre>
 +
 
 +
 
 +
==FastLMM==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>]
  
 
To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>statgen-setup login --tutorial gemini
+
<pre>statgen-setup login --tutorial fastlmm-gcta
 
</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].
 
  
==GenABEL==
+
==Fine-mapping (SuSiE method)==
* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
* [[GeneABEL Exercise|Exercise Commands]]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]
  
To install from packages, follow the configuration steps above and run the following command.
 
  
<pre>sudo apt-get install genabel-tutorial</pre>
+
To run the exercise from docker image provided,
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.
+
 
 +
<pre>statgen-setup launch --tutorial finemap
 +
</pre>
 +
 
 +
==GCTA==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>]
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup login --tutorial fastlmm-gcta
 +
</pre>
 +
 
 +
 
 +
==Gemini==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup login --tutorial gemini
 +
</pre>
 +
 
  
 
==Genehunter==
 
==Genehunter==
Line 89: Line 96:
  
 
==GWAS: Data Quality Control==
 
==GWAS: Data Quality Control==
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
  
====Installing Packages====
+
To run the exercise from docker image provided,
To install from packages, follow the configuration steps above and run the following command.
+
 
 +
<pre>statgen-setup login --tutorial plink
 +
</pre>
  
<pre>sudo apt-get install plink-tutorial</pre>
 
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==
 
==GWAS: Association Analysis Controlling for Population Substructure==
* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
  
====Installing Packages====
+
To run the exercise from docker image provided,
To install from packages, follow the configuration steps above and run the following command.
+
  
<pre>sudo apt-get install plink-tutorial</pre>
+
<pre>statgen-setup login --tutorial plink
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.
+
</pre>
  
==Homozygosity Mapper==
 
  
 +
==Homozygosity Mapper==
 
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
 
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
 
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
 
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
Line 115: Line 121:
  
 
==IGV==
 
==IGV==
* [http://statgen.us/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
 
 
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>]
 
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>]
 
* [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==
Line 135: Line 135:
 
</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==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>]
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup login --tutorial pleiotropy
 +
</pre>
 +
 
 +
 
 +
==Polygenic risk prediction (NPS method)==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
 +
 
 +
To run the exercise from docker image provided,
 +
 
 +
<pre>statgen-setup login --tutorial nps
 +
</pre>
 +
 
 +
 
 +
==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.
 +
 
  
 
<!--
 
<!--
Line 153: Line 188:
 
</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==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc PSEQ Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
* [[PSEQ Commands in Exercise|Exercise Commands]]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>]
  
 
To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
 +
 +
<pre>statgen-setup launch --tutorial pseq
 +
</pre>
 +
 +
Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,
  
 
<pre>statgen-setup login --tutorial pseq
 
<pre>statgen-setup login --tutorial pseq
 
</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==
Line 175: Line 230:
 
</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==
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
 
* [[RV-TDT|Exercise Commands]]
 
* [[RV-TDT|Exercise Commands]]
  
Line 214: Line 268:
 
To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>statgen-setup login --tutorial slink
+
<pre>statgen-setup login --tutorial slink</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].
+
 
+
 
+
  
 
==SUPERLINK==
 
==SUPERLINK==
Line 226: Line 275:
  
 
==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/handout/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].
+
Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.
 
+
==VAT Mendelian==
+
* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [[VAT mendelian commands|Exercise Commands]]
+
 
+
 
+
To install from packages, follow the configuration steps above and run the following command.
+
 
+
<pre>sudo apt-get install vtools-mendelian-tutorial</pre>
+
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.
+

Revision as of 16:45, 9 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.

General instructions


Tutorial specific instructions

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.

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.

Alohomora

Annovar complex traits

To run the exercise from docker image provided,

statgen-setup login --tutorial annovar

Annovar Mendelian traits

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


Fine-mapping (SuSiE method)


To run the exercise from docker image provided,

statgen-setup launch --tutorial finemap

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 launch --tutorial pseq

Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,

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

SUPERLINK

Variant Association Tools


To run the exercise from docker image provided,

statgen-setup launch --tutorial vat

Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.