I had an existing instance that still had data on it from my PyRad analysis on 20160727 that I needed to retrieve.
Logged into Amazon AWS via the web interface and started my existing instance (via the Actions > Instance State > Start menu). After the instance started and generated a new public IP address, I SSH’d into the instance:
ssh -i "/full/path/to/bioinformatics.pem" firstname.lastname@example.org
NOTE: I needed the full path to the PEM file! Tried multiple times using a relative path (e.g. ~/Documents/bionformatics.pem) and received error messages that the file did not exist and “Permission denied (public key)”.
Changed to the directory with the PyRAD analysis and created a tarball to speed up eventual download from the EC2 instance to my local computer:
tar -cvzf 20160715_pyrad_analysis.tar.gz /home/ubuntu/data/analysis/
After compression, I used secure copy to copy the file from the EC2 instance to my local computer:
scp -i "/full/path/to/bioinformatics.pem" email@example.com:/home/ubuntu/data/20160715_pyrad_analysis.tar.gz /Volumes/toaster/sam/
This didn’t work initially because I attempted to transfer the file using Hummingbird (instead of my computer). The SSH connection kept timing out. The reason for this was that I hadn’t previously used Hummingbird to connect to the EC2 instance and Hummingbird’s IP address wasn’t listed in the Security Groups table as being allowed to connect. I made that change using the Amazon AWS web interface:
Once transfer was complete, I terminated the EC2 instance and the corresponding data volume.