Linux Fall 2020 Schedule

	Topics	Reading (TLCL)	Assignments
Week 1:
Tuesday Aug 25	Course introduction The terminal Navigating the file system Paths	Chapters 1, 2	Assignment 1 due Sept 1
Thursday Aug 27	Options Working with files I - more, less, head, tail, wc Making & removing Copying & moving Wildcards Getting help	Chapter 3 (ls, less) Chapters 4-5	Assignment 2 due Sept 1
Week 2:
Tuesday Sept 1	Downloading files Redirection Working with files II - cat, grep, cut Pipes More pipes	Chapter 3 (file) Chapter 6 Chapter 16 Chapter 18 (gzip) Chapter 20 (sort, uniq, cut)	Assignment 3 due Sept 8
Thursday Sept 3	Working with files III - sed, tr Aliasing and chaining Intro to bash scripting Making scripts executable Best practices Extras on Permissions	Chapter 5 (alias) Chapter 9 Chapter 20 (sed) Chapter 24	Assignment4 due Sept 8
Week 3:
Tuesday September 8	Variables Download script Conditionals	Chapter 25 (Variables and Constants)	Assignment 5 due Sept 15
Thursday September 10	Capturing Command Output Loops and Script Variables	Chapter 27	Assignment 6 due Sept 15
Week 4:
Tuesday September 15	Working on Summit Job submission BWA Vignette	Chapter 16 (ssh) Summit Guide
Thursday September 17	Putting everything together Installing Software Packages with conda
ExamProject:
Tuesday September 22			Turn in Exam Project by 10am

Computational biology at CSU