Learning to use HPC clusters, R Markdown & GitHub pages

I had just spent the last 3 weeks or so trying to figure out how to use R on the university’s HPC clusters, and thought it would be helpful to produce a guide to help other beginners as well. I wrote it using R Markdown, since I thought I might as well learn how to write in R Markdown better at the same time.

To turn it from a R Markdown (rmd) file to something others can see, I had several options, as pdf or as html. I could convert it to a pdf, and either share it with the lab or put it up somewhere online. The conversion to pdf produced problems with image placement (the images would be placed somewhere else from where I wanted them to be, so that things would fit nicely on the pages). I didn’t want to learn the hack (incorporating some LaTeX formatting etc.) so I thought I could just leave it as a local html which opens on my browser and then use ‘Save as PDF’ to turn it to a pdf. That removed some formatting and didn’t look very nice either.

I found out I could use the RWordpress package to publish the html file rendered to my WordPress site, which I tried (and actually published briefly for about 20 hours before I took it down from this site). Apart from broken image links which I had to fix manually by uploading my images to the media gallery here, it worked quite alright. The formatting wasn’t as nice perhaps, especially the bits with the code, but it worked.

Then I thought about it a bit more and decided perhaps I should learn how to publish it on my GitHub, because then it’ll be easier to make changes to the code and have the website all synced to changes. So I did! I’m quite pleased to have learned this now, it’s been quite fun writing in markdown language and mastering git a bit more. Here’s the guide if you’re interested. 

Yeast and yia yia

Do you think we’re mad …
when we say we spray down every package that
comes through the post;
that we wipe every pack of vegetables, cans of tomatoes and beans, bottles of milk, boxes of cereal;
wash our hands after touching the door knob;
all in a bid to hide
from an invisible 
virus.

This lockdown period has made it difficult for usual carers and relatives of my partner’s grandma (yia yia in Greek, pronounced ya ya) to help, so being the least vulnerable in the family, we’ve been spending weekends and some week nights helping how we can. Her being of a grand old age (>90 years old), we’re being ultra careful ourselves to not inadvertently catch and pass on anything. This extra alertness and care exerts a mental load, one that has now been normalised into the background. I look forward to not having to spray anti-bacterial (does it work for viruses though…) solutions on everything at some point in the future.

It is curious how we as humans exist in a world with so many creatures invisible to our naked eye, and celebrate some but vilify others. Our household has been having a go at making sourdough bread, keeping with the times. The starter seems to be thriving well, a concoction of yeast and beneficial bacteria. We’ve learned to harness their potential and ‘control’ them, and so find them less threatening. Yet should we seek to exterminate those that lie beyond our control, and may do us harm? To eliminate all harmful viruses and bacteria (as though that were possible in the first place), insects (like mosquitoes and flies) and whatever else that displeases us?

Struggles with getting the too-wet dough to shape. Many thanks and gratitude to my patient younger brother who dispenses bread-making and bread-saving advice across time zones.