==Running Tutorials on Your Computer==
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 ===General instructions===* [https://github.com/statgenetics/statgen-courses/wiki/How-to set it up and run -launch-course -tutorials #alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer, using these docker images and optionally a utility script we created ]* [https://github.com/statgenetics/statgen-courses/wiki/How-to streamline various docker commands-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=Tutorial specific instructions===<code>SoS</code> requires Python 3.6+ to run. It is recommended that you install We use a script [https://docs.condagithub.iocom/enstatgenetics/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/sosstatgen-docscourses/running.html here for alternative installation methods] if you have troubles with that command. To install <code>docker<blob/code> from command line please follow our instructions [http:master/src/statgen.us/lab-wiki/orientation/jupytersetup "statgen-setup.html#install-docker here"]. Alternatively Mac users can download to start the docker app based environments for Mac and install from a graphical interfacethese tutorials. Please refer to the previous section for instructions on the installation of this script.
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===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 Command "statgen-setup login" will allow you to start and other features provided by our utility script please read here our [https://githublogin to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells.com/statgenetics/This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-courses/blob/master/README.md complete documentation setup launch" which will start a JupyterLab server to perform the utility script]analysis.
==Alohomora==
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
==AnnotationAnnovar complex traits==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx pdf Functional Annotation Exercise <nowiki>[DOCXPDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
</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 MEndelianMendelian traits==
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
==Cochran Armitage Trend Test==
<pre>statgen-setup login --tutorial epistasis
</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].
</pre>
The "==Fine-mapping (SuSiE method)==* [https://github.com/statgenetics/statgen-setup" script is available courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/srchandout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]* [https://github.com/statgenetics/statgen-setup herecourses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>] and can be installed following * [https://github.com/statgenetics/statgen-courses/blob/master/READMEnotebooks/finemapping_answers.md#prepareipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-yoursetup launch -computer-to-manage-the-tutorials these instructions].tutorial finemap</pre>
==GCTA==
</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==
<pre>statgen-setup login --tutorial gemini
</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].
==GWAS: Data Quality Control==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.docx pdf Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]
To run the exercise via JupyterLab from docker image provided,
<pre>statgen-setup login launch --tutorial plink
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and Alternatively, you can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-opt to-manage-run the-tutorials these instructions].exercise via command terminal from docker image provided,
<pre>statgen-setup login --tutorial plink
</pre>
==GWAS: Association Analysis Controlling for Population Substructure==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.docx pdf Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
To run the exercise via JupyterLab from docker image provided,
<pre>statgen-setup login launch --tutorial plink
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and Alternatively, you can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-opt to-manage-run the-tutorials these instructions].exercise via command terminal from docker image provided,
<pre>statgen-setup login --tutorial plink
</pre>
==Homozygosity Mapper==
* [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==
</pre>
The "statgen-setup" script is available ==LD clumping==* [https://github.com/statgeneticscumc/statgen-coursesbioworkflows/blob/master/srcGWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup here] and can be installed following launch --tutorial clumping</pre> ==MR-JTI for TWAS==* [https://github.com/statgenetics/statgen-courses/blob/master/READMEnotebooks/MR_JTI.md#prepareipynb MR-yourJTI Exercise <nowiki>[IPython Notebook]</nowiki>] '''Under Development''' To run the exercise from docker image provided, <pre>statgen-computersetup login -to-manage-the-tutorials these instructions].tutorial twas</pre>
==Pleiotropy==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.docx pdf Pleiotropy Exercise <nowiki>[DOCXPDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.docx pdf Pleiotropy Answers to Questions <nowiki>[DOCXPDF]</nowiki>]
To run the exercise from docker image provided,
</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)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.docx pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
To run the exercise from docker image provided,
</pre>
The "statgen-setup" script is available ==Polygenic risk prediction (LDpred2 method)==* [https://github.com/statgenetics/statgen-courses/blob/master/srchandout/statgen-setup hereldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF] and can be installed following </nowiki>]* [https://github.com/statgeneticscumc/statgen-coursesbioworkflows/blob/master/READMEldpred/ldpred2_example.md#prepareipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-yoursetup launch -computer-tutorial ldpred2</pre> Then follow prompts on the terminal output toopen 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-manage-data</pre> to load thedata-tutorials these instructions]set to the JupyterLab workspace.
<!--
</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==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc pdf PSEQ Exercise <nowiki>[DOCXPDF]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Commands in Exercise|Exercise Commands<nowiki>[Ipython Notebook]</nowiki>]
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>
The " ==R and PLINK== To run the exercise from docker image provided, <pre>statgen-setup" script is available launch --tutorial plink-r-nothnagel</pre> ==REGENIE==* [https://github.com/statgenetics/statgen-courses/blob/master/srchandout/statgen-setup hereregenie_example.pdf REGENIE Exercise <nowiki>[PDF] and can be installed following </nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/READMEnotebooks/regenie_example.md#prepareipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-yoursetup launch -computer-tutorial regenie</pre> Then follow prompts on the terminal output toopen 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-manage-data</pre> to load thedata-tutorials these instructions]set to the JupyterLab workspace.
==Regression==
</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==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exercise_v3RV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial slink</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==
==Variant Association Tools==
* [https://statgenetics.github.iocom/statgenetics/statgen-courses/notebooksblob/master/handout/VAT.html docx VAT Exercise <nowiki>[HTMLDOCX]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Commands in Exercise|Exercise Commands<nowiki>[Ipython notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup login launch --tutorial vat
</pre>
The "statgen-setup" script is available [https://githubThen follow the prompts on the terminal output to open up the JupyterLab server in your web browser.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] You should find the exercise notebook in the side panel, and you can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-click to-manage-the-tutorials these instructions]open it.
