Presentation

The presentation slides are available -- PPTX and PDF.

Tutorial instructions

1. Find your machine name at this link and save it in a notepad.
2. Download amazon.pem and save it to your computer as a .PEM file.
3. Log in: Windows instructions or Mac OS X instructions. Use username 'ubuntu', not 'root'; pull machine names from here.
4. Execute sudo bash to change to the super-user account once you're logged in.
5. The first time only,

   mkdir /mnt/data
   ln -fs /mnt/data /data
   cd /data
   curl -O http://public.ged.msu.edu.s3.amazonaws.com/mrnaseq-subset.tar
   tar xvf mrnaseq-subset.tar
   

6. Optionally, install dropbox.
7. For mRNAseq, start at the Eel Pond protocol Note: if you want to start at the diginorm stage (#2), you can type:

   cd /mnt/work
   curl -O http://public.ged.msu.edu.s3.amazonaws.com/mrnaseq-extract-qc.tar
   tar xf mrnaseq-extract-qc.tar
   

8. Later in the day, we may do the variant calling tutorial.

Running things on your own Ubuntu 12.04 machine

Follow the apt-get instructions here to install the necessary components to run these tutorials on your own. You'll need to start with a blank Ubuntu 12.04 machine.

Other links to look at:

• Starting up your own Amazon computer. Note, use ami-59a4a230 (Ubuntu 12.04 LTS)
• Instructions (see the apt-get stuff) on configuring machines for khmer-protocols: here.
• Variant calling tutorial