Goals - July 2016

Unfortunately, most of this month’s goals are the same as last months!

  • Process Olympia oyster GBS data. I’ve been running two different analyses (Stacks and PyRad) on two different machines (Hummingbird and Roadrunner, respectively) and I keep encountering different problems! For example, just yesterday, the following popped up in Terminal on my SSH connection to a Docker container on Roadrunner running PyRad in a Jupyter Notebook (click on the image to enlarge):


The computer became completely unresponsive (for the second time in less than 24hrs). Maybe the problem is Docker. Maybe it’s creating a remote tunnel to a Docker container. Maybe it’s running Jupyter Notebook through a remote tunnel into a Docker container? I don’t know. At this point, I’ll just install PyRad directly on Roadrunner and try to get the analysis done that way. It certainly isn’t convenient because it means I have to be physically present at Roadrunner to execute commands and check on things…

  • Get stuff running on Amazon AWS and Hyak as soon as possible. I think the increased computing power will improve my chances to actually complete the Oly GBS analysis due to the greater stability those computing environments provide.

  • Quantify coral DNA methylation. This should be straightforward and completed on Tuesday, 20160705.