Syllabus

Course Objectives: Unix is a powerful set of computing tools which allow the user to develop customized programs for data reduction and analysis. The system can be quite daunting as basic proficiency requires learning at least 20 - 30 commands and real proficiency can require much more. In fact, some people ACTUALLY hate UNIX. (note the source of this broadside, BTW).  In reality, Unix is one of those things, like life, which appears endless in its potential compexity. Just when you think you have it figured out, something new comes along.

Having scared you with that, the exciting aspect of Unix is that with basic proficiency you can do custom programming that was previously only available to real programming whizzes. With computing power being so inexpensive and increasing at such a rapid rate, you don't even have to develop into a particularly elegant programmer to get REAL work done.

The primary goal of this course is to provide the basic tools necessary for each student to develop custom tools suited to their data. Everyone will learn a collection of basic tools and how to combine them to make more specialized tools. Each student will then develop expertise in specific tools related to the specific sorts of data they use(or hope to use) in their research

      Principle source materials

COURSE SCHEDULE

Class Session	Topics
1	Class introduction: Description of Emory computers and Unix system. Operating systems, Shells and programming. Description of files and directories, File permissions  Introduction remote display and Web resources. File creation Commands: man, pwd , cd, chmod, ls, passwd, env, vi
2	Manuals (man). Special characters, redirection of output (>) and input (<), stdin, stdout, pipes (|), mv, cp, rm , rmdir, mkdir Job Control (^z, bg fg), processes (ps)
3	Customizing your environment: .profile, .kshrc, alias Command line editing using vi ; finding files (find) Scripts, shell variables, positional parameters, pattern recognition (grep family); minimal formatting, pr, nice
4	Shell programing: scripts, filename substitution, Positional parameters, user input, test command; File system navigation - links (ln) Combining files and extracting columns: cut , paste , and join
5	Shell programming: Flow control - for loops, if - then - else, case, select (menu creation)
6	Shell Programming: Arrays, more flow control, User interface
7	Combining pattern recognition with shell scripts: grep, fgrep, egrep, sed. Special utilities: file, head, tail,
8	Data extraction: AWK, NAWK, GAWK
9	Data Extraction: Control statements in AWK
10	AWK arrays and transformations
11	The last of AWK and interaction between AWK and other programs
12	Connecting UNIX output to other programs
13-15	Individual projects: Consultation