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 https://github.com/R4EPI/sitrep. 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.
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 👍.