Short Course on Systems Genetics 2015
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Short Course on Systems Genetics 2015

This is a repository for Short Course on Systems Genetics (9/27 - 10/02/2015) at The Jackson Laboratory that includes the following tutorials:

  • kallisto, EMASE & g2gtools (KB Choi & N Raghupathy) [markdown]: generate an index, pseudo-align reads and quantify the expression
  • DESeq2 (N Raghupathy) [markdown]: detect differential expression between groups of RNASeq samples
  • DOQTL (D Gatti) [markdown]: kinship matrix, linkage and association mapping, eQTL viewer
  • Mediation analysis (S Munger, P Simecek & G Churchill) [markdown1] [markdown2] [markdown3]: find an intermediate between genotype and trans-regulated gene/protein
  • D3 viewers: eQTL, pQTL

The participants use their web browsers to connect to customized Docker containers hosted on Digital Ocean virtual machines (see screen captures below).

rstudio | terminal

Docker is a lightweight container virtualization platform. We created three Docker images for this course: churchill/doqtl (RStudio, DOQTL, DESeq2), churchill/asesuite (kallisto, EMASE) and churchill/webapp (eQTL/pQTL viewer). You can run docker containers on your computer or in the cloud environments like AWS, Digital Ocean, Microsoft Azure or Google Cloud. Dockerfiles can also serve as a list of instructions how to install the software on your computer.

How to start Digital Ocean droplet?

Here, I will give a description how our virtual machines have been created. You can either create a machine manually on Digital Ocean, SSH to it and start the docker containers. Or you can use R/analogsea package to start a droplet from a command line.

In both cases, first, create an account on Digital Ocean. You should get $10 promotional credit that currently corresponds to free 3.5 days of 8GB machine running expense.

For beginners - create a virtual machine manually

  • Log into your Digital Ocean account. Click on "Create Droplet" button. Choose any droplet hostname and select its size - 8GB memory, 4 CPU, $0.119/hour.

Droplet size

Scroll down to "Select image", click on 'Applications' tab and select Docker. Click on "Create Droplet" button. Droplet now starts in 1-2 minutes. You should receive an email with a password.

Docker button

  • Note down your droplet's IP.ADDRESS. SSH into your droplet (ssh root@IP.ADDRESS) and pull docker images
  docker pull rocker/hadleyverse
  docker pull churchill/doqtl
  docker pull churchill/asesuite
  docker pull ipython/scipystack
  docker pull churchill/webapp
  • Next, download the required datasets (~30 minutes)
  • Finally, run docker containers.
  docker run -d -v /data:/data -p 8787:8787 -e USER=rstudio -e PASSWORD=sysgen churchill/doqtl
  docker run -dt -v /data:/data -p 43210:43210 -p 43211:43211  churchill/asesuite
  docker run -dt -v /data:/data -p 8888:8888 -p 8889:8889 churchill/webapp /usr/bin/

For advanced users - create a virtual machine with R/analogsea package

Access your virtual machine in the web browser

In your browser you can now access RStudio at http://IP.ADDRESS:8787 (user: rstudio, password: sysgen) and the terminal at http://IP.ADDRESS:43210 (user: root, password: sysgen). The eQTL and pQTL viewers are running at http://IP.ADDRESS:8888 and http://IP.ADDRESS:8889, respectively.

You are paying for your Digital Ocean machine as long as it is running. Do not forget to destroy it when you are done!