Resource for Genotype-by-Sequencing in Ecology and Evolution workshop
During this session, we will learn to be comfortable with the command line. First, we will log in to the server Mahuika, a computing resource maintained by the New Zealand eScience Infrastructure (NeSI).
You might have managed to log in to NeSI already. If you have not, please request help from one of us and we will assist you.
Next, we will hop across to the bit of Mahuika we are using for this workshop using (note, the l following v is a lower case “L” not a one!):
ssh -Y ga-vl01
Once you have jumped on to ga-vl01 using the commands above, get into the space created for you for this workshop by using the cd (change directory) command (don’t worry - we are going to go through commands like cd in more detail in a sec!):
cd /nesi/nobackup/nesi02659/users/<yourusername>
NeSI has a ton of different projects for a bunch of researchers around the motu (country). The project we are using for this workshop is nesi02659. You might notice nesi02659 is in the “path” shown in the cd command above. We are going to cover paths to files and folders in just a minute!
For this session, we will use material created under a Creative Commons license by The Carpentries. The Carpentries teaches foundational coding and data science skills to researchers worldwide. The Carpentries is active in New Zealand and @Otago, we encourage you to keep your eyes open for local events.
We will go through the following carpentries lessons together:
We have now gone through the basics of the command line. Let’s reinforce some of what we just learnt in this final exercise.
Learning the command line might seem hard at first but it gets a lot easier with a little bit of practice! As well as the resources we just covered, here are a few more to help you out if you get stuck:
If you learn better in person with other folks, please check out the events run by Otago Carpentries, Otago Study Group, and Otago Mohio (a South Campus spin-off of Otago Study Group):