User contributions

Jump to: navigation, search
Search for contributions
 
 
      
 
   

(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)

  • 17:51, 28 April 2017 (diff | hist) . . (+2,440)‎ . . Samtools ‎
  • 00:07, 28 April 2017 (diff | hist) . . (+103)‎ . . Qualimap ‎ (current)
  • 00:01, 28 April 2017 (diff | hist) . . (+937)‎ . . Qualimap ‎
  • 15:40, 26 April 2017 (diff | hist) . . (+185)‎ . . Qualimap ‎
  • 15:36, 26 April 2017 (diff | hist) . . (+234)‎ . . N Qualimap ‎ (Created page with "= Introduction = Inspecting bam files for quality = Installation = Has a number of dependencies: * optparse (available from CRAN) * NOISeq, Repitools, Rsamtools, GenomicFe...")
  • 15:09, 26 April 2017 (diff | hist) . . (+217)‎ . . Samtools ‎
  • 12:00, 26 April 2017 (diff | hist) . . (+16)‎ . . Main Page ‎
  • 23:38, 19 April 2017 (diff | hist) . . (+966)‎ . . N Hdi2u S25 ‎ (Created page with "= Accessing a running program or working with others interactively = * If you just run a job and then close down the terminal you ran it from, normally the job will be termin...") (current)
  • 23:38, 19 April 2017 (diff | hist) . . (+538)‎ . . N Hdi2u S24 ‎ (Created page with "= Processes = * Sometimes a command or program you run in the terminal goes on too long, or is obviously doing something you did not plan. * If there is no obvious way (such...") (current)
  • 23:38, 19 April 2017 (diff | hist) . . (+385)‎ . . N Hdi2u S23 ‎ (Created page with "= Environment Variables = * We have seen that the way commands run can be modified by the options passed on the command line. * One of the most important variables is PATH. T...") (current)
  • 23:37, 19 April 2017 (diff | hist) . . (+793)‎ . . N Hdi2u S22 ‎ (Created page with "* Try the command: grep "^DE" hsy14768.embl and grep -x "DE.*" hsy14768.embl * What are the <code>^</code> symbol and the <code>-x</code> parameter in these commands doing? *...") (current)
  • 23:37, 19 April 2017 (diff | hist) . . (+830)‎ . . N Hdi2u S21 ‎ (Created page with "= Grep = * grep stands for "global regular expression print" * you use this command to search for text patterns in a file, for example, Linux's mini-dicitonary. grep "adge"...") (current)
  • 23:36, 19 April 2017 (diff | hist) . . (+262)‎ . . N Hdi2u S20 ‎ (Created page with "= Piping output between applications = * <code>|</code>, often called an operator because it's so powerful * not always easy to find on the keyboard == Exercise == * "Pipe" t...") (current)
  • 23:36, 19 April 2017 (diff | hist) . . (+1,235)‎ . . N Hdi2u S19 ‎ (Created page with "= Removing files and directories = * The key difference between deleting something from the command line and using the graphical file browser is that in the first case the fi...") (current)
  • 23:36, 19 April 2017 (diff | hist) . . (+352)‎ . . N Hdi2u S18 ‎ (Created page with "= Linking to files = * copying big files can exhaust hard disk quickly. * You can instead create a link to it with the <code>ln -s</code> command. ln -s current.file linktoc...") (current)
  • 23:35, 19 April 2017 (diff | hist) . . (+1,381)‎ . . N Hdi2u S17 ‎ (Created page with "= Copying files and directories = * The basic command used to copy files using the command line is <code>cp</code>. * At a minimum, you must specify two arguments: the name o...") (current)
  • 23:35, 19 April 2017 (diff | hist) . . (+1,425)‎ . . N Hdi2u S16 ‎ (Created page with "== Getting by in only normal mode == * movement keys, "w" jump via start of words; "e" jump via ends; "fc" jump to next c * "0" for start of line, "A" for end of line and int...") (current)
  • 23:35, 19 April 2017 (diff | hist) . . (+1,203)‎ . . N Hdi2u S15 ‎ (Created page with "= Text editing = * There are very many text editors, but one of the most powerful and dependable is <code>vi</code>. * It has a steep but tiny learning curve, which we hope t...") (current)
  • 23:34, 19 April 2017 (diff | hist) . . (+648)‎ . . N Hdi2u S14 ‎ (Created page with "== Remember the man pages == There are many command line options available for each of the above commands, as well as functionality we do not cover here. To read more about th...") (current)
  • 23:34, 19 April 2017 (diff | hist) . . (+1,212)‎ . . N Hdi2u S13 ‎ (Created page with "= Reading text files = * These are useful when you want to look at the contents of a file, but not edit it. * Among the most common of these commands are <code>cat</code>, <c...") (current)
  • 23:33, 19 April 2017 (diff | hist) . . (+1,249)‎ . . N Hdi2u S12 ‎ (Created page with "= Command history = * This is another very handy tool for saving typing * Previous commands you have used are stored in your "history". * You use the up and down arrow keys t...") (current)
  • 23:32, 19 April 2017 (diff | hist) . . (+1,265)‎ . . N Hdi2u S11 ‎ (Created page with "= Tab completion = * Fear of the command line often means, fear of typing too much. Everybody fears this, so there are tools. * Tab completion is probably the most important...") (current)
  • 23:32, 19 April 2017 (diff | hist) . . (+1,271)‎ . . N Hdi2u S10 ‎ (Created page with "= Changing directories = * Directories are the same as folders. In linux "directory" is more common. * Directories within directories are called subdirectories" * The command...") (current)
  • 23:31, 19 April 2017 (diff | hist) . . (+908)‎ . . N Hdi2u S09 ‎ (Created page with "= Linux shortcut symbols = * We've seen <code>*</code> is a special symbol, and how useful it can be. * There are more however: * <code>?</code> matches a single character l...") (current)
  • 23:30, 19 April 2017 (diff | hist) . . (+765)‎ . . N Hdi2u S08 ‎ (Created page with "= Basic Linux tips for filenames = * Linux does not deal well with spaces in filenames * Expect problems when transferring files from Windows. * Everything is case sensitive...") (current)
  • 23:30, 19 April 2017 (diff | hist) . . (+440)‎ . . N Hdi2u S07 ‎ (Created page with "Now try: man ls * Did you think you knew this command already? * What does the <code>-h</code> option do? What about the <code>-a</code> option? What would running <code>ls...") (current)
  • 23:29, 19 April 2017 (diff | hist) . . (+42)‎ . . Hdi2u S06 ‎ (current)
  • 23:28, 19 April 2017 (diff | hist) . . (+854)‎ . . N Hdi2u S06 ‎ (Created page with "= Learning about Linux commands = * This is a continuous and very important activity * Linux has a large and comprehensive documentation system called <code>man</code> * Linu...")
  • 23:28, 19 April 2017 (diff | hist) . . (+883)‎ . . N Hdi2u S05 ‎ (Created page with "== Answers == * You get the hidden files * the <code>-l</code> is the long listing * this file is empty, it has no content. * by default ls will list files anywhere it can fi...") (current)
  • 23:27, 19 April 2017 (diff | hist) . . (+972)‎ . . N Hdi2u S04 ‎ (Created page with "= Listing files and directories = * <code>ls</code> is the most common command of all. It lists files and folders in your current location. * By default it requires no argume...") (current)
  • 23:27, 19 April 2017 (diff | hist) . . (+928)‎ . . N Hdi2u S03 ‎ (Created page with "= Navigating the command line = * Bioinformatics tools can have very many options * They also can be combined with many others, leading to very long command-line. * You do no...") (current)
  • 23:26, 19 April 2017 (diff | hist) . . (+1,096)‎ . . N Hdi2u S02 ‎ (Created page with "= Anatomy of a Command = <command> <options/parameters> <arguments> * <command> what do I want to do? * <options/parameters> how do I want to do it? * <arguments>, on what...") (current)
  • 23:26, 19 April 2017 (diff | hist) . . (-1,098)‎ . . Hdi2u S01 ‎ (current)
  • 23:25, 19 April 2017 (diff | hist) . . (-22,344)‎ . . Hdi2u S01 ‎
  • 23:25, 19 April 2017 (diff | hist) . . (+24,146)‎ . . N Hdi2u S01 ‎ (Created page with "= The Command-line (shell) = The real power of Linux/Unix systems is the command line. * Many programs and facilities are available through graphical options on Linux, but a...")
  • 23:24, 19 April 2017 (diff | hist) . . (+24,146)‎ . . N Hdi2u S00 ‎ (n) (current)
  • 22:47, 19 April 2017 (diff | hist) . . (+2,967)‎ . . N Hdi2u intro ‎ (Created page with "= Course schedule = * This is a cut-down version of 1 day course. * History and theory has been left out * Scripting is excluded (although plenty of one-liners) * Maximise pr...") (current)
  • 17:34, 19 April 2017 (diff | hist) . . (+3,839)‎ . . N Hdi2u dirorg exercise ‎ (n) (current)
  • 14:45, 19 April 2017 (diff | hist) . . (+1,497)‎ . . Hdi2u rendertotsv exercise ‎ (current)
  • 14:37, 19 April 2017 (diff | hist) . . (+4,589)‎ . . N Hdi2u rendertotsv exercise ‎ (n)
  • 14:34, 19 April 2017 (diff | hist) . . (-1,969)‎ . . Hdi2u commandbased exercises ‎ (current)
  • 14:30, 19 April 2017 (diff | hist) . . (+26,115)‎ . . N Hdi2u commandbased exercises ‎ (Created page with "= The Command-line (shell) = The real power of Linux/Unix systems is the command line. * Many programs and facilities are available through graphical options on Linux, but a...")
  • 14:29, 19 April 2017 (diff | hist) . . (+30)‎ . . Main Page ‎
  • 22:02, 17 April 2017 (diff | hist) . . (+321)‎ . . One-liners ‎ (current)
  • 21:42, 17 April 2017 (diff | hist) . . (+250)‎ . . One-liners ‎
  • 00:09, 15 April 2017 (diff | hist) . . (-2,136)‎ . . Biolinux Source course ‎ (current)
  • 23:55, 14 April 2017 (diff | hist) . . (-9,484)‎ . . Biolinux Source course ‎
  • 18:53, 14 April 2017 (diff | hist) . . (-601,958)‎ . . Biolinux Source course ‎
  • 18:51, 14 April 2017 (diff | hist) . . (+430)‎ . . Course itself ‎ (current)
  • 17:21, 14 April 2017 (diff | hist) . . (0)‎ . . Main Page ‎

(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)

Retrieved from "http://stab.st-andrews.ac.uk/wiki/index.php/Special:Contributions/Rf"