index.qmd

# Welcome! {.unnumbered}

Welcome to the website for the National Marine Fisheries Service
Linux, Slurm, and Bioinformatics training to be held virtually
over three days:

* Day 1: Monday, October 17, 2022. 10 AM - 12 PM PDT
* Day 2: Tuesday, October 18, 2022. 10 AM - 12:30 PM PDT
* Day 3: Wednesday, October 19, 2022. 10 AM - 12 PM PDT


## Prerequisites

This course will be using the Sedna high-performance computing
cluster located at the Northwest Fisheries Science Center. This cluster
(and, hence, this course)
is only available to NMFS employees and affiliates. If you are a NMFS
employee and you are interested in this course, please see 
[here](https://docs.google.com/document/d/1nn0T0OWEsQCBoCdaH6DSY69lQSbK3XnPlseyyQuU2Lc/edit#heading=h.qpx57rvxr0sj) for information about how to
get an account on the cluster. 

This course is intended for people who have already had some exposure
to Unix or Linux.  You should be reasonably comfortable navigating around 
the Unix filesystem using the command line.
For a refresher, please read [this chapter from my
online bioinformatics book](https://eriqande.github.io/eca-bioinf-handbook/essential-unixlinux-terminal-knowledge.html).

My goal is to:

- teach the shell programming constructs and
the text processing tricks that I find myself using all the time in my 
day-to-day work
- provide an introduction to how to use SLURM to do cluster computing
- On the last day, show how Snakemake works, and how it can be used on the
Sedna cluster to simplify your bioinformatics life.

## Course Topics and Sessions


* Day 1: Intro, Unix-review, shell programming, `awk`
    - Introduction to the Sedna cluster (15 minutes Krista and Giles)
        - Cluster infrastructure and configuration.
        - Scientific software and the installation requests
    - [Quick Unix Review](nmfs-bioinf/quick-unix-review.qmd#quick-unix-review) (25 minutes)
    - [Shell Programming](nmfs-bioinf/shell-prog.qmd#shell-prog) (50 Minutes)
    - [A Brief `awk` Intro](nmfs-bioinf/awk-intro.qmd#awk-intro)  Processing text files with `awk` (30 minutes)
* Day 2: A little bash stuff, then Sedna and SLURM
    - [Bash scripts and functions](nmfs-bioinf/scripts-and-functions.qmd#script-func) (20 minutes)
    - [Sedna and SLURM intro](nmfs-bioinf/slurm.qmd#ssintro) (40 minutes) 
    - [Submitting jobs with `sbatch`](nmfs-bioinf/sbatch.qmd#sbatch) (40 minutes)
    - [Slurm Job Arrays](nmfs-bioinf/slurm-arrays.qmd#slurm-arrays) (40 minutes)
* Day 3: Job Arrays, then an introduction to Snakemake
    - [Slurm Job Arrays](nmfs-bioinf/slurm-arrays.qmd#slurm-arrays) (25 minutes)
    - [Snakemake Tutorial Introduction](nmfs-bioinf/snake.qmd#snake) (90 minutes)