So, been an interesting day. Lots of frustrations with computers, but I built something kind of cool (and mostly useless) for
as a proof of concept for some future work.
First, the computer stuff.
I’ve been tasked with getting a couple of the slave nodes on the X-serve cluster running in standalone mode. Originally this seemed like a relatively straight forward task. However, I’ve come across multiple issues.
- The X-serve runs an older version of OS X, Mountain Lion to be specific. I had access to a copy of the installer, a new hard drive to install it on, and an external drive enclosure, so I should be good to go, right? Not so much.
First I found that my laptop, with OS X Sierra running, would’t let me install an older version of OS X on to the external drive. So with the help of Sam, we hustled up an older Mac Mini lying around, running Lion. Then I was faced with an error that the installer wouldn’t work because it was sourced from an unverified soure (Eagle). Annoying. I think I have a work around that involves using Restore in Disk Utility and unpackaging the Installer to find the .dmg file. I would test this, but neither the Mac Mini, nor my laptop will recognize the external enclosure. Will troubleshoot this more tomorrow.
- Disk Utility times out when trying to image the Nodes
I was trying to clone the drives from the custer nodes to preserve the data on them, but Disk Utility was having none of that. Every time I tried to set up a clone job, I would get an error code 60, which has something to do with the connection timing out. After much googling, I was unable to find what this exactly meant, so I did a direct copy between the two drives. I will hold off on any formatting of the node hard drives until I make sure this is an acceptable way to back up data.
Now for the fun stuff!
The trim job I set Hummingbird on over the weekend completed, so I started the assembly process. I wanted to take a picture of the terminal screen, but apparently Platanus sucks up every spare resource in the virtual machine, so getting the screenshot off/ posting it to github seems to be more than it can handle at the moment. Platanus’s assembly UI also leaves a little to be desired as it gives no hint on a progress or time to completion. I guess I just come back periodically to see if it’s encountered an error, or completed.
The command used to start was ./platanus assemble -o Oly -f *.fa_trimmed
Also, I’ve started experimenting with Shiny. Shiny is a web application development tool for the R programming language.
It allows you to create interactive data visualizations hosted on the web. Way fancier than the typical results of a
par(mfrow = c(3,3) or whatever paneled plot in R.
In the coming weeks I’ll have some data from satellite tagged sablefish with temperature, depth, and location information. I want to come up with some interesting ways for people to view and explore this data, and I felt Shiny was a good avenue for this.
I found some open source time series data on CO2 measurements at Mauna Loa to act as a proxy, and tossed in a map that a user can define boundaries for, as well as place a point just for fun. Link to the app and the code can be found below.