Cloud Genomics: Instructor Notes

Cloud Genomics Pre-Workshop

Using the cloud genomics lesson materials may involve using Amazon EC2 instances. To get this up and running, do the following:

• Find out how many learners you are expecting. Contact your host for this information. You will likely want to have a couple extra instances lying around in case one dies.
• Start an etherpad for the workshop.
• Contact Tracy with the dates of your workshop, a link to the etherpad and the number of learners expected. She will start the instances, and they will appear in your etherpad.

VM Image Directories A high-level listing of the directory tree from the dcuser account is shown below. Please note that is may be subject to change over time, but we’ll try to remember to update this doc.

dcuser@ip-172-31-50-230:~$ tree -L 2
.
├── dc_sample_data
│   ├── r_genomics
│   ├── sra_metadata
│   └── untrimmed_fastq
├── Desktop
│   ├── firefox.desktop
│   ├── gnome-terminal.desktop
│   ├── nautilus.desktop
│   └── rstudio.desktop
├── Downloads
├── FastQC
│   ├── Configuration
│   ├── fastqc
│   ├── fastqc_icon.ico
│   ├── Help
│   ├── INSTALL.txt
│   ├── jbzip2-0.9.jar
│   ├── LICENSE.txt
│   ├── net
│   ├── org
│   ├── README.txt
│   ├── RELEASE_NOTES.txt
│   ├── run_fastqc.bat
│   ├── sam-1.103.jar
│   ├── Templates
│   └── uk
├── openrefine-2.6-beta.1
│   ├── licenses
│   ├── LICENSE.txt
│   ├── README.txt
│   ├── refine
│   ├── refine.ini
│   ├── server
│   └── webapp
├── R
│   └── x86_64-pc-linux-gnu-library
└── Trimmomatic-0.32
    ├── adapters
    ├── LICENSE
    └── trimmomatic-0.32.jar

21 directories, 19 files

During the workshop

We had a couple instances die as we were going through our workshop.

• First, check that this isn’t an issue with the student’s network settings. Try and load a different website to verify that their internet is working.
• Try to connect to the instance on a different machine, or with a different protocol. For instance, if the student is working in PuTTy, try to connect using scp.
• Try to ping the instance like so:

ping hostname

• If the student’s internet is working, you can’t connect via a different protocol or you can’t ping the instance, probably it’s died. Assign the student to a new instance. We had 2 out of ~30 die at our workshop at ISU.