We’ve got our instance up and running, now it’s time to put some files there. We need data to make this all work!
I’m using Laura’s stress related geoduck reference proteome as my example, but this should work with anything.
First, SSH in to your EC2 instance and make some directories where you’ll put stuff.
Those look like some directories. Next we need to copy stuff over. I use
scp to copy everything over, since I have copies on my local hard drive. You can use curl, wget, or whatever you like.
Those are some files! Next I install percolator.
the pertinent command being
dpkg -i percolator-v3-01-linux-amd64.deb
Next, we install pecan.
I didn’t take as many screenshots of this, but it’s referenced in other posts. Short take: Unzip pecan, edit the config file located in
/pecan/PECAN/PecanUtil to look like:
Your proteome file names and locations may change, but the idea is the same.
then go to
/pecan/ and run
sudo python setup.py install. After a brief time, the build completes and you should be able to test things by running bare commands
Success! Now on to configuring Starcluster/Open Grid Engine. The not fun part of all of this.