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We have created a debian repository to make it easier to use our tutorialsStarting Fall 2019 we adopt [https://www. This repository allows you to install all required software and example data included in tutorials on your computerdocker. Using this repository will require that you have administrator access com/ docker] to a computer with Linux Systemrun our course material . If you don't We 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 created various [https://wwwhub.vultrdocker.com/ VULTRu/statisticalgenetics docker repositories]. Second, you can install a Virtual Machine program (such as with source material freely available from [https://wwwgithub.virtualbox.orgcom/ VirtualBoxstatgenetics/statgen-courses github]) on your computer, for users to readily setup and then load reproduce our pre-configured virtual machine image (VM Image) into the Virtual Machinetutorials on their own computers. You These docker images can refer also be used as production tool to these online videos [[VirtualBox Installation|here]] to install VirtualBox run relevant software on your computer(Mac, Linux or Windows) for your own data analysis.

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 In this document we will focus on discussing how to change set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to whatever you likestreamline various docker commands.

To ===Pre-requisites===Software you need to install the repository on the cloud server, virtual machine, or your own computer, you need are <code>SoS</code> (a workflow system to follow these configuration steps. Please run as the root user or using the sudo commandour course utility script) and <code>docker</code>.

====Mac and Linux users====<precode>echo "deb SoS</code> requires Python 3.6+ to run. It is recommended that you install [trusted=yeshttps://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/deb .lab-wiki/" | sudo tee 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:/etc/apt/sourcesraw.listgithubusercontent.dcom/statgenetics/statgen.listsudo add-aptcourses/master/src/statgen-repository setup <code>src/statgen-y ppa:webupd8teamsetup</javasudo aptcode>] to your <code>PATH</code> and change it to executable, eg, <code>chmod +x ~/bin/statgen-get updatesetup</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.

We have made a video tutorial ===Tutorial specific instructions===Material and instructions for specific exercise are listed in each section below (''only those using statgen-setup command are relevant to show you how our docker based tutorials''). They provide links to install the repository step materials and a minimal set of commands to use for launching and running an exercise. For advanced options and other features provided by step which is available our utility script please read here our [https://www.youtubegithub.com/watch?v=5jRJHXxkC9g&t=19s here]statgenetics/statgen-courses/blob/master/README. If you want md complete documentation to install specific exercise at your demands, please refer to commands listed in each section belowthe utility script].

* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]

<pre>docker pull statisticalgenetics/annovarstatgen-setup login --tutorial annovar

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_revisedArmitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]

==Epistasis (PLINK and CASSI)==Result Files* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Epistasis_PLINK_CASSI.pdf Epistasis exercise <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <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].   ==FastLMM==:* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.uspdf FastLMM exercise <nowiki>[PDF]</filesnowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</2016pre> The "statgen-setup" script is available [https:/07/gatk_resultsgithub.tarcom/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.gz GATKcom/IGV statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. ==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> 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].

* [https://drive.googlegithub.com/filestatgenetics/dstatgen-courses/0B2pJ9cgevF3sTS1DeGxYalFTN00blob/view Bam files for master/handout/Gemini.docx Gemini exercise<nowiki>[DOCX]</nowiki>]

==GenABEL==To run the exercise from docker image provided,* <pre>statgen-setup login --tutorial gemini</pre> The "statgen-setup" script is available [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/genabelblob/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]<master/nowiki>src/statgen-setup here]* and can be installed following [[GeneABEL Exercise|Exercise Commands]https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-qccourses/blob/master/handout/PLINK_data_QC_V2PLINK_data_QC.pdf docx Exercise <nowiki>[PDF]</nowiki>]

====Installing Packages====To install run the exercise from packagesdocker image provided, follow the configuration steps above  <pre>statgen-setup login --tutorial plink</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and run the can be installed following command[https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. 

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-substructurecourses/blob/master/handout/GWAS_Data_Controlling_for_Substructure_V2PLINK_Substructure.pdf docx Exercise <nowiki>[PDF]</nowiki>]

====Installing Packages====To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.

<pre>sudo aptstatgen-setup login -get install plink-tutorialplink</pre>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== *The "statgen-setup" script is available [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/Homozygosity_mapping_exercise_part_1.pdf Exercise Part Isrc/statgen-setup here]*and can be installed following [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]*[http:blob/master/wwwREADME.homozygositymapper.org Data Setsmd#prepare-your-computer-to-manage-the-tutorials these instructions].

  ==IGVHomozygosity Mapper== *[httpshttp://statgen.researchus/files/tutorials/Homozygosity_mapping_exercise_part_1.bcmpdf Exercise Part I]* [http://statgen.eduus/files/softwaretutorials/igv/igv-2Homozygosity_mapping_exercise_part_2.3pdf Exercise Part II]* [http://www.97homozygositymapper.jar igv.jar Software Linkorg Data Sets] ==IGV==*[https://statgengithub.research.bcmcom/statgenetics/statgen-courses/blob/master/handout/IGV.edudocx IGV exercise <nowiki>[DOCX]</filesnowiki>]* [http:/2017/09statgen.us/datafiles/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 VCF Filescan be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].

* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.uspdf LINKAGE Exercise <nowiki>[DOCX]</filesnowiki>]  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial mlink</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-tutorialsthese instructions]. ==Pleiotropy==* [https:/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_numgithub.pdf Linkage Introduction com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.docx Pleiotropy Exercise <nowiki>[PDFDOCX]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.docx Pleiotropy Answers to Questions <nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial pleiotropy</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 PRS NPS Exercise <nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial nps</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].

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/Popgen_exe_ansmaster/handout/PopGen.pdf docx Popgen Exercise <nowiki>[PDFDOCX]</nowiki>]*  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial popgen</pre> The "statgen-setup" script is available [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_drift.q R Script for popgen_driftmaster/src/statgen-setup here]* and can be installed following [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_selectionmaster/README.q R Script for popgen_selectionmd#prepare-your-computer-to-manage-the-tutorials these instructions].

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercise_2019master/handout/PSEQ.pdf doc PSEQ Exercise <nowiki>[PDFDOCX]</nowiki>]

To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.

<pre>sudo aptstatgen-setup login -get install plinkseq-tutorialpseq</pre> The exercise's files will then "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed in the folder ''following [https:/home/sharedgithub.com/pseq''statgenetics/statgen-courses/blob/master/README. You can run from there or copy the files into md#prepare-your user's home directory and proceed with -computer-to-manage-the exercise-tutorials these instructions].

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]

To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.

<pre>sudo aptstatgen-setup login -get install regression-tutorialregression</pre> The exercise's files will then "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed in the folder ''following [https:/home/sharedgithub.com/regression''statgenetics/statgen-courses/blob/master/README. You can run from there or copy the files into md#prepare-your user's home directory and proceed with -computer-to-manage-the exercise-tutorials these instructions].

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exercise_v3RV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/seqsparkhandout/slink_ex_shortSlink.pdf doc SLINK Exercise <nowiki>[PDFDOCX]</nowiki>]

* [httphttps://statgenstatgenetics.usgithub.io/filesstatgen-courses/tutorialsnotebooks/vat/VAT_exercise_2019_1_nographsVAT.pdf html VAT Exercise <nowiki>[PDFHTML]</nowiki>]

<pre>sudo apt-get install vtools-tutorial</pre>The exercise's files will then be installed in the folder ''/home/shared/vat''. You can To run from there or copy the files into your user's home directory and proceed with the exercise. ==VAT Mendelian==* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]* [[VAT mendelian commands|Exercise Commands]]from docker image provided,

To install from packages, follow the configuration steps above and run the following commandThe "statgen-setup" script is available [https://github. <pre>sudo aptcom/statgenetics/statgen-get install vtools-mendelian-tutorial<courses/pre>The exercise's files will then blob/master/src/statgen-setup here] and can be installed in the folder ''following [https:/home/sharedgithub.com/statgenetics/statgen-courses/blob/master/vat''README. You can run from there or copy the files into md#prepare-your user's home directory and proceed with -computer-to-manage-the exercise-tutorials these instructions].