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1 Virtual Machine Anyone have problems installing it? VM: Virtual Box - allows you to run a different operating system within the current operating system of your machine. Linux flavor : Debian Everything (except slides) preinstalled for you

2 BTI Bioinformatics Course 2013 Syllabus 3/19 Intro to Linux PartI Linux background info Commandline basics Navigating the file system 3/26 Intro to Linux Part II: Commandline Operations Useful commandline operations 4/2 Web tools vs Command line Advantages and disadvantages of each 4/9 Introduction to RNAseq What information can be gained by RNA-seq experiments Overview of experimental design 4/16 RNAseq assembly Overview of Tophat2 pipeline Demonstration with example tomato data 4/23 RNAseq analysis Detection of differential expression with Cufflinks 4/30 Introduction to R Why use R? R basics 5/7 R graphs Plotting RNA-seq results with Cummerbund GO analysis (if time allows)

3 BTI Bioinformatics Course Intro to Linux 3/19/2013 Susan Strickler Room 217

4 What is Linux? Open source Unix-like operating system Runs on a wide variety of system architectures including servers, super computers, cell phones over 300 distributions actively developed

5 What is Linux? Kernel released by Linus Torvald in 1991

6 What is Linux? Both graphical user interface (GUI) and command line interface

7 Why use Linux? Free to use. Stable and secure can edit and enhance source code world-wide community of developers Can be installed on just about anything Many bioinformatics programs will not run on Windows

8 Linux Distributions Distributions have been created around the Linux kernel Many distros available (distrowatch.com) Examples: RedHat Debian (we will use this) Ubuntu

9 The Shell Runs in a terminal Command line - where commands are typed and executed Different types - we will use bash

10 Linux Filesystem hierarchical filesystem Folders (directories in UNIX-speak) are separated by / / is the root Paths starting with / are absolute (ex: /etc/apt/sources.list) Paths not starting with / are relative ( ex: Desktop/ ) to the current directory ~/ denotes the home directory, for example /home/bioinfo/.. refers to the folder above the current folder Files starting with a. are not readily visible (.bashrc)

11 Linux Filesystem Navigation pwd - shows current working directory ls - list files in current working dir

12 Linux Filesystem Navigation cd - change directory, go to Data cd - go up a level

13 Linux Filesystem Navigation cd - autocompletion (tab) cd - go to root

14 Linux Filesystem Navigation cd - go to home dir

15 Linux Filesystem Layout Main higher-level system dirs (exact layout depends on distribution Paths not starting with / are relative (ie Desktop/ ) to the current directory /bin & /lib - code and code libraries /usr - more code and libraries /var - logs and other data /home user directories, eg. /home/bioinfo/ *we will mainly deal with this dir /tmp - temporary files /etc - configuration information /proc - special file system

16 Linux Command $ls -lh /home Command line prompt command Simple option flag Argument

17 Linux Command When in doubt how to use a command, follow it with --help ex: ls --help Man pages are the documentation for Linux commands $ man <command> $ man ls

18 Linux Command Today: commands on left side of handout Next time: right side of sheet

19 Linux Commands find a file with the extension.zip * is a wild card

20 Linux Commands locate a file with the extension.zip How is this different from find?

21 Linux Commands cp copy a file to the Desktop autocompletion (tab)

22 Linux Commands mkdir make a directory called unix2

23 Linux Commands mv move a file into a directory

24 Linux Commands touch make an empty file named test

25 Linux Commands mv rename the test file to practice *mv is used both to move a file/directory and change the name of a file/directory

26 Linux Commands rm remove a file

27 Linux Commands make a directory called test rmdir remove the test directory * can also use rm -r but be careful with this command

28 Other useful commands Interrupting, terminating execution (control-z, control-c) Background/foreground jobs (bg, fg, &) ex: locate *.*

29 Other useful commands History (up arrow key, control-r, history) clear go to beginning of commandline control-a go to end of commandline control-e

30 Redirection STDIN is the keyboard by default STOUT is the screen by default STDIN and STOUT can be changed by redirection: locate *.txt > files.txt tr '[:lower:]' '[:upper:]' < files.txt > out.file

31 File Naming Typically contain alphanumberic characters (lower case), underscores, hyphens, and periods. Avoid: backslashes, spaces, quotes, foreign letters README - often contains important information about files in that directory (ex: when downloading programs) INSTALL - information about installing programs

32 Processes Every running program is treated as a process Every process has a process ID top - Shows all processes as a self updating list ps - Outputs process information to STDOUT. ps -elf kill - terminate process Linux: The /proc filesystem every number is a dir corresponding to a running process. ls /proc

33 Disk and Memory Management df - amount of disk space used and available free - amount of memory used and available

34 Text Editing: EMACS Why not use MS Word? Embedded characters no auto indenting, syntax highlighting

35 Using EMACS Command: emacs Opens a new window if X-window system present Save file: control-x control-s Close program: control-x control-c Cancel operation: control-g Search forward: control-s

36 File Compression tar groups or ungroups files tar -xvf ungroups.tar files gzip compresses files gunzip decompresses.gz files unzip decompresses.zip file unzip unix_class_file_samples.zip bzip2 compresses files bunzip2 decompresses.bzip2 files pbzip2 compresses files, multi-threaded

37 Useful Links

38 Exercises What directories are in the home directory? create a directory called test_dir on the desktop make three files in test_dir, test1, test2.txt, testb2.txt remove all the files in test_dir with the.txt extension with one command find the zip file called ch4_demo_dataset.tar.gz copy the file to the Desktop decompress the file ungroup the files we will use these files in a future class

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