Tag Archives: software install

Software Install – samtools-0.1.19 and stacks-1.37

Getting ready to analyze our Ostrea lurida genotype-by-sequencing data and wanted to use the Stacks software.

We have an existing version of Stacks on Hummingbird (the Apple server blade I will be running this analysis on), but I figured I might as well install the latest version (stacks-1.37).

Additionally, Stacks requires samtools-0.1.19 to run, which we did NOT have installed.

I tracked all of this in the Jupyter (iPython) notebook below.

Due to permissions issues during installation, I frequently had to leave the Jupyter notebook to run “sudo” in bash. As such, the notebook is messy, but does outline the necessary steps to get these two programs installed.

Jupyter notebook: 20160406_STACKS_install.ipynb

NBviewer: 20160406_STACKS_install.ipynb


Computer Setup – Dell Optiplex 960 for OA System

Dan had been using the Dell Studio XPS 7100 for running LabView to record data from the Honeywell Dual Input Controller for controlling the OA system at Manchester. The computer occasionally failed; it would shutdown, wouldn’t boot and would just produce six steady beeps. Although this behaviour was inconsistent, Dan needs a computer that will always remain on for data logging.

Our departmental computer support person couldn’t diagnose the problem and offered to provide a replacement computer, but only if we purchased a SSD drive for the replacement computer (at a cost of ~$250 for a 480GB SSD drive and adapter).

So, instead of wasting the money (and the continued headache of dealing with our computer support person), I grabbed the Dell Optiplex 980 from FSH 240, backed up the data on that computer (backed up to Nate’s folder on our server: backupordie). I obtained the appropriate license/serial numbers for LabView from the College of Engineering, downloaded and installed LabView 2014 and service pack 1 (SP1).

The old computer was able to boot, so I copied all the LabView files that Dan had previously been using to the Friedman Lab Dropbox and then downloaded them to the Dell Optiplex 980. Additionally, I re-seated the RAM sticks in hopes of making the computer usable again. I have moved this computer to FSH 240 to take the place of the Dell Optiplex 980.

Dan will take the newly configured Dell Optiplex 960 to Manchester to use as a data logger for the Honeywell Dual Input Analyzer and its pH and temp data.