EC2 and You, pt. 2: Uploading files and installing stuff

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.

Screen Shot 2017-03-14 at 10.55.52 AM

Screen Shot 2017-03-14 at 10.56.00 AM

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.

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Screen Shot 2017-03-14 at 11.04.21 AM

Those are some files! Next I install percolator.

Screen Shot 2017-03-14 at 11.07.51 AM

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:

Screen Shot 2017-03-14 at 11.37.20 AM

Your proteome file names and locations may change, but the idea is the same.

then go to /pecan/ and run sudo python install. After a brief time, the build completes and you should be able to test things by running bare commands

Screen Shot 2017-03-14 at 11.40.09 AM

Success! Now on to configuring Starcluster/Open Grid Engine. The not fun part of all of this.