Changes
From Statistical Genetics Courses
==Running Tutorials on Your Computer==
We have created a debian repository to make it easier to use our tutorialsadopted [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 since Fall 2019. 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]) 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, and then load our pre-configured virtual machine image (VM ImageLinux or Windows) into the Virtual Machinefor your own data analysis. You can refer In this section we will discuss how to these online videos [[VirtualBox Installation|here]] to install VirtualBox 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.
====Mac and Linux users==== <precode>echo "deb SoS</code> requires Python 3.6+ to run. It is recommended that you install [trusted=yes] https://statgendocs.usconda.io/deb 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</" | sudo tee -a code> to install <code>SoS</etccode>, or, check out [https:/apt/sourcesvatlab.listgithub.dio/statgensos-docs/running.html here for alternative installation methods] if you have troubles with that command.listsudo addTo install <code>docker</code> please follow our instruction [http://statgen.us/lab-aptwiki/orientation/jupyter-repository setup.html#install-y ppadocker here]. Additionally please download our utility script [https:webupd8team/javasudo apt/raw.githubusercontent.com/statgenetics/statgen-get updatecourses/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.
==Alohomora==
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial annovar
</pre>
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial gemini
</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== *[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://www.homozygositymapper.org Data Sets]
==IGV==
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial igv
</pre>
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial mlink
</pre>
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial popgen
</pre>
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial pseq
</pre>
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial regression
</pre>
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].
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial vat
</pre>
