UNIX
These lectures teach the UNIX command line, shell scripting, and running analyses on the UCR HPCC cluster. They build on each other, so work through them in order.
| Lecture | Class | Topics | |
|---|---|---|---|
| I | Logging In and Command Line Basics (PDF) | Sep 24 | the cluster, logging in, OnDemand, paths and navigation, viewing files, getting help, shortcuts, nano, your first shell script |
| II | Files, Data and Running Programs (PDF) | Sep 29 | copying and moving, wildcards, symbolic links, permissions, quotas, redirection and pipes, grep, compression, downloading and transferring data, modules, interactive jobs, Git for homework |
| III | Shell Programming (PDF) | Oct 1 | variables and quoting, conditionals, loops, functions, robust scripts, looping over samples |
| III lab | Data Processing with Pipes (PDF) | lab / reading | grep, cut, sort/uniq, tr, paste, join, sed, awk; answering questions about GFF and BLAST tables |
| IV | Running Analyses on the Cluster (PDF) | Oct 29 | SLURM batch jobs, choosing resources, job arrays, storage, tmux, conda and containers, find/xargs/parallel |
See also the SSH keys guide and the Git and GitHub guide.
