command line

Things I Learned About 2-Factor Authentication on GitHub

Since the end of 2018, I’ve been a part of a collaboration between RECON and MSF called the R4EPIs initiative where we are trying to integrate a more standardized workflow of R for field epidemiologists so that it can be more cost-effective (no license fees) and troubleshooting among epidemiologists can be more effective. We have a repository to host templates for automated situation reports at When we created the GitHub organisation, we wanted to make sure that the code being submitted to the repository was genuinely authored by the person and didn’t contain malware from a hijacked account1, so we required 2-factor authentication for the R4EPI github organisation from the start.

Installing the ABySS

A couple of weeks ago, I wanted to explore assembling 55 genomes of Sclerotinia sclerotiorum to check for structural rearrangements that could be caused by sub-lethal fungicide exposure. I figured the best way to do this was to assemble these genomes de novo as opposed to aligning them to a reference. This brought me to installing the ABySS de novo assembler on the HCC Tusker Cluster… and I can happily report, that after half a day of command line bullshittery1, I had ABySS up and running 👍.