Short Course on Systems Genetics 2015
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
docker
figures
markdown
scripts
LICENSE
README.md

README.md

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)
   wget https://raw.githubusercontent.com/churchill-lab/sysgen2015/master/scripts/download_data_from_ftp.sh
   /bin/bash download_data_from_ftp.sh
   rm download_data_from_ftp.sh
  • 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/start-app.sh

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!