Introduction to Bio-Linux 6
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Introduction to For Bio-Linux 8 December 2015 Website: http:// environmentalomics.org /bio-linux Email: [email protected] Table of Contents PART ONE: INTRODUCTION TO THE BIO-LINUX 8 SYSTEM............................................1 Logging in and exploring the Bio-Linux desktop...............................................................................................................1 Running applications..........................................................................................................................................................3 Finding files and drives......................................................................................................................................................3 Setting things up.................................................................................................................................................................4 Finding your way on the system..........................................................................................................................................7 The Root Folder....................................................................................................................................................................7 Using the command shell......................................................................................................................................................8 Anatomy of a Command....................................................................................................................................................9 Listing files in a directory................................................................................................................................................10 Learning about Linux commands.....................................................................................................................................11 Basic Linux tips for filenames.........................................................................................................................................12 Getting the prompt back when running graphical applications from the terminal..........................................................12 Linux shorthand and shortcuts.........................................................................................................................................13 More Basic Linux Commands...........................................................................................................................................13 Changing directories........................................................................................................................................................14 Tab completion.................................................................................................................................................................15 Command history................................................................................................................................................................17 Making a directory...........................................................................................................................................................17 Office software....................................................................................................................................................................18 Using text editors.................................................................................................................................................................19 Nano.................................................................................................................................................................................19 Gedit.................................................................................................................................................................................19 Reading text files.................................................................................................................................................................20 An important note on line endings – CR and LF.............................................................................................................21 Copying files........................................................................................................................................................................22 Linking to files.....................................................................................................................................................................23 Removing files and directories...........................................................................................................................................24 Redirecting output to files..................................................................................................................................................25 Piping output between applications..................................................................................................................................26 Diff, Grep and Sort.............................................................................................................................................................27 Diff...................................................................................................................................................................................27 Grep..................................................................................................................................................................................27 Environment Variables.......................................................................................................................................................29 Changing permissions on files and directories.................................................................................................................30 Some other useful information..........................................................................................................................................31 Copying and pasting text..................................................................................................................................................31 The simple way to stop a process.....................................................................................................................................31 Putting a command to one side........................................................................................................................................31 Logging out of a session..................................................................................................................................................31 Clearing your terminal of text..........................................................................................................................................31 Accessing a running program or working with others interactively................................................................................32 Accessing your machine – including a full graphical desktop - remotely.......................................................................32 PART TWO: INTRODUCTION TO BIOINFORMATICS ON BIO-LINUX.............................33 Documentation and Help for Bioinformatics Software on Bio-Linux...........................................................................33 Bio-Linux Bioinformatics Documentation......................................................................................................................33 Help Functions within the Programs................................................................................................................................34 Example data for this tutorial............................................................................................................................................34 Interface choices..................................................................................................................................................................35 General points about working with bioinformatics programs.......................................................................................36 Sequence formats.............................................................................................................................................................36 File naming conventions in bioinformatics......................................................................................................................37 Naming files and the danger of over-writing previous results.........................................................................................39 A common problem: what is a text file and what is not...................................................................................................39 GZipped files in bioinformatics.......................................................................................................................................40 EXAMPLES OF RUNNING BIOINFORMATICS PROGRAMS ON BIO-LINUX..................41 Analysing sequences with QIIME.....................................................................................................................................41 Preparation.......................................................................................................................................................................42