Introduction to UNIX Command Line

Home , Alias (command), Bash (Unix shell), Cd (command), Command (Unix), Diff, Echo (command)

● Files and directories ● Some useful commands (echo, cat, grep, find, diff, tar) ● Redirection ● Pipes ● Variables ● Background processes ● Remote connections (e.g. ssh, wget) ● Scripts

The Command Line

● What is it? ● An interface to UNIX ● You type commands, things happen ● Also referred to as a “shell” ● We'll use the bash shell – check you're using it by typing (you'll see what this means later): ● echo $SHELL ● If it doesn't say “bash”, then type bash to get into the bash shell

Files and Directories

home var usr

mcuser abenson drmentor

science catvideos stuff

data code report

M51.fits simulate.c analyze.py report.tex

Files and Directories

● Get a pre-made set of directories and files to work with ● We'll talk about what these commands do later ● The “$” is the command prompt (yours might differ). Type what's listed after hit, then press enter.

$$ wgetwget http://bit.ly/1TXIZSJhttp://bit.ly/1TXIZSJ -O-O playground.tarplayground.tar

$$ tartar xvfxvf playground.tarplayground.tar

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

“Present Working Directory”

$$ pwdpwd Shows the full path of your current /home/abenson/home/abenson location in the filesystem. $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd “Change Directory” /home/abenson/home/abenson $$ cdcd playgroundplayground Change to a new directory – relative to $$ pwdpwd current location unless you give a full /home/abenson/playground/home/abenson/playground path $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd “LiSt” /home/abenson/playground/home/abenson/playground $$ lsls List the content of the current directory. animalsanimals documentsdocuments sciencescienceShows both directories and files. $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground “MaKe DIRectory” $$ lsls animalsanimals documentsdocuments sciencescience Make a new directory in the current $$ mkdirmkdir mystuffmystuff directory $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls Options “-l” to ls requests a long badger.txtbadger.txt porcupine.txtporcupine.txt listing. $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $$ lsls Options “-l” to ls requests a long badger.txtbadger.txt porcupine.txtporcupine.txt listing. $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ pwdpwd /home/abenson/home/abenson $$ cdcd playgroundplayground $$ pwdpwd /home/abenson/playground/home/abenson/playground $$ lsls animalsanimals documentsdocuments sciencescience $$ mkdirmkdir mystuffmystuff $$ lsls animalsanimals documentsdocuments mystuffmystuff sciencescience $$ cdcd animals/mammalsanimals/mammals $ ls e $ ls s es m on yt ti e badger.txtbadger.txtsi porcupine.txtporcupine.txt b n m is p in tio a $ ls m-l r u e a n $ lser -l se ro iz re ile totaltotalP 88 U G S C F -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt

Files and directories

$$ lsls -a-a ...... badger.txtbadger.txt porcupine.txtporcupine.txt $$ cdcd .. $$ pwdpwd /home/abenson/playground/animals/mammals/home/abenson/playground/animals/mammals $$ cdcd .... $$ pwdpwd /home/abenson/playground/animals/home/abenson/playground/animals $$ cdcd $$ pwdpwd /home/abenson/home/abenson $$ cdcd ~~ $$ pwdpwd /home/abenson/home/abenson

Files and directories

$$ cdcd ~/playground/animals/mammals/~/playground/animals/mammals/ $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ lsls -l-l totaltotal 88 -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $$ chmodchmod go+wgo+w badger.txtbadger.txt $$ lsls -l-l totaltotal 88 -rw-rw-rw-.-rw-rw-rw-. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $$ cpcp badger.txtbadger.txt super_badger.txtsuper_badger.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_badger.txtsuper_badger.txt $$ mvmv super_badger.txtsuper_badger.txt super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_mellivorinae.txtsuper_mellivorinae.txt

Files and directories

$$ cdcd ~/playground/animals/mammals/~/playground/animals/mammals/ $ ls $ ls “CHange MODe” badger.txtbadger.txt porcupine.txtporcupine.txt $ ls -l $ ls -l Changes permissions for the file: totaltotal 88 u = user -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt g = group -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt = other $$ chmodchmod go+wgo+w badger.txtbadger.txt o $$ lsls -l-l totaltotal 88 +-= – add, remove, set -rw-rw-rw-.-rw-rw-rw-. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson rwx13471347 – read,MayMay write,3131 18:0518:05 execute porcupine.txtporcupine.txt $$ cpcp badger.txtbadger.txt super_badger.txtsuper_badger.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_badger.txtsuper_badger.txt $$ mvmv super_badger.txtsuper_badger.txt super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_mellivorinae.txtsuper_mellivorinae.txt

Files and directories

$$ cdcd ~/playground/animals/mammals/~/playground/animals/mammals/“CoPy” $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt Make a copy of a file – you give the $$ lsls -l-l name of the original file, followed totaltotal 88 by the new file. -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $$ chmodchmod go+wgo+w badger.txtbadger.txt $$ lsls -l-l totaltotal 88 -rw-rw-rw-.-rw-rw-rw-. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $$ cpcp badger.txtbadger.txt super_badger.txtsuper_badger.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_badger.txtsuper_badger.txt $$ mvmv super_badger.txtsuper_badger.txt super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_mellivorinae.txtsuper_mellivorinae.txt

Files and directories

$$ cdcd ~/playground/animals/mammals/~/playground/animals/mammals/ $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $ ls -l $ ls -l “MoVe” totaltotal 88 -rw-r--r--. 1 abenson abenson 1944 May 31 18:03 badger.txt -rw-r--r--. 1 abenson abensonMove 1944 (rename) May 31 a file18:03 – you badger.txt give the -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $ chmod go+w badger.txt name of the original file, followed $ chmod go+w badger.txt by the new name. $$ lsls -l-l totaltotal 88 -rw-rw-rw-.-rw-rw-rw-. 11 abensonabenson abensonabenson 19441944 MayMay 3131 18:0318:03 badger.txtbadger.txt -rw-r--r--.-rw-r--r--. 11 abensonabenson abensonabenson 13471347 MayMay 3131 18:0518:05 porcupine.txtporcupine.txt $$ cpcp badger.txtbadger.txt super_badger.txtsuper_badger.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_badger.txtsuper_badger.txt $$ mvmv super_badger.txtsuper_badger.txt super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt super_mellivorinae.txtsuper_mellivorinae.txt

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ manman lessless NAMENAME lessless -- oppositeopposite ofof moremore

SYNOPSISSYNOPSIS lessless -?-? lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless “echo” NAMENAME lessless -- oppositeopposite ofof moremore Write the given text to screen (or somewhere else – more of this SYNOPSISSYNOPSIS later). lessless -?-? lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless “conCATenate” NAMENAME lessless -- oppositeopposite ofof moremore Take the content of all files listed, join them together, and write it out. SYNOPSISSYNOPSIS lessless -?-? lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless “conCATenate” NAMENAME lessless -- oppositeopposite ofof moremore Take the content of all files listed, join them together, and write it out. SYNOPSISSYNOPSIS lessless -?-? lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless “more” NAMENAME lessless -- oppositeopposite ofof moremore Display contents of a file to terminal with pagination (use return or space SYNOPSISSYNOPSIS to step through). lessless -?-? lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless “less” NAMENAME lessless -- oppositeopposite ofof moremore Fancy version of more. Scroll SYNOPSISSYNOPSIS forward and backward. Search (“/”), lessless -?-? etc. lessless --help--help

Useful Commands

$$ echoecho "Hello?"Hello? CanCan youyou hearhear me?"me?" Hello?Hello? CanCan youyou hearhear me?me? $$ catcat badger.txtbadger.txt “MANual” BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ catcat badger.txtbadger.txt porcupine.txtporcupine.txtShow documentation for a command. BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... PorcupinesPorcupines areare rodentsrodents withwith aa coatcoat ofof sharpsharp spines...spines... $$ moremore badger.txtbadger.txt BadgersBadgers areare short-leggedshort-legged omnivores...omnivores... $$ lessless badget.txtbadget.txt BadgersBadgers areare short-leggedshort-legged omnivores…omnivores… $$ manman lessless NAMENAME lessless -- oppositeopposite ofof moremore

SYNOPSISSYNOPSIS lessless -?-? lessless --help--help

Useful Commands

$$ grepgrep skunkskunk badger.txtbadger.txt membersmembers ofof thethe skunkskunk family,family, placingplacing $$ grepgrep rodentrodent *.txt*.txt porcupine.txt:Porcupinesporcupine.txt:Porcupines areare rodentsrodents porcupine.txt:Porcupinesporcupine.txt:Porcupines areare thethe third-largestthird-largest ofof thethe rodents,rodents, $$ cdcd $$ findfind playgroundplayground -name-name "*.txt""*.txt" playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt playground/animals/mammals/badger.txtplayground/animals/mammals/badger.txt playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txt playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt $$ findfind playgroundplayground -type-type dd playgroundplayground playground/documentsplayground/documents playground/animalsplayground/animals playground/animals/mammalsplayground/animals/mammals playground/animals/reptilesplayground/animals/reptiles playground/scienceplayground/science

Useful Commands

$$ grepgrep skunkskunk badger.txtbadger.txt membersmembers ofof thethe skunkskunk family,family, placingplacing $$ grepgrep rodentrodent *.txt*.txt porcupine.txt:Porcupinesporcupine.txt:Porcupines areare rodentsrodents porcupine.txt:Porcupinesporcupine.txt:Porcupines areare thethe third-largestthird-largest ofof thethe rodents,rodents, $$ cdcd $ find playground -name "*.txt" $ find playground -name "*.txt" “Get Regualr ExPression” playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt playground/animals/mammals/badger.txt playground/animals/mammals/badger.txtSearch for a word (or words) in a file. playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txt playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt $$ findfind playgroundplayground -type-type dd playgroundplayground playground/documentsplayground/documents playground/animalsplayground/animals playground/animals/mammalsplayground/animals/mammals playground/animals/reptilesplayground/animals/reptiles playground/scienceplayground/science

Useful Commands

$$ grepgrep skunkskunk badger.txtbadger.txt membersmembers ofof thethe skunkskunk family,family, placingplacing $$ grepgrep rodentrodent *.txt*.txt porcupine.txt:Porcupinesporcupine.txt:Porcupines areare rodentsrodents porcupine.txt:Porcupinesporcupine.txt:Porcupines areare thethe third-largestthird-largest ofof thethe rodents,rodents, $$ cdcd $$ findfind playgroundplayground -name-name "*.txt""*.txt" playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt playground/animals/mammals/badger.txtplayground/animals/mammals/badger.txt playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txt playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt $$ findfind playgroundplayground -type-type dd playgroundplayground Wildcards playground/documentsplayground/documents playground/animalsplayground/animals “*” matches any sequence of characters playground/animals/mammalsplayground/animals/mammals “?” matches any single character playground/animals/reptilesplayground/animals/reptiles playground/scienceplayground/science

Useful Commands

$$ grepgrep skunkskunk badger.txtbadger.txt membersmembers ofof thethe skunkskunk family,family, placingplacing $$ grepgrep rodentrodent *.txt*.txt porcupine.txt:Porcupinesporcupine.txt:Porcupines areare rodentsrodents porcupine.txt:Porcupinesporcupine.txt:Porcupines areare thethe third-largestthird-largest ofof thethe rodents,rodents, $$ cdcd $$ findfind playgroundplayground -name-name "*.txt""*.txt" playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt playground/animals/mammals/badger.txtplayground/animals/mammals/badger.txt playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txt playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt $$ findfind playgroundplayground -type-type dd playgroundplayground “find” playground/documentsplayground/documents playground/animalsplayground/animals Search a path for files/directories that playground/animals/mammalsplayground/animals/mammals match some specification playground/animals/reptilesplayground/animals/reptiles playground/scienceplayground/science

Redirection

$$ rmrm super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ cdcd playground/animals/mammals/playground/animals/mammals/ $$ catcat badger.txtbadger.txt >> another_badger.txtanother_badger.txt $$ lsls another_badger.txtanother_badger.txt badger.txtbadger.txt porcupine.txtporcupine.txt $$ catcat >> list_of_mammals.txtlist_of_mammals.txt batbat catcat ocelotocelot camelcamel ^D^D $$ catcat list_of_mammals.txtlist_of_mammals.txt batbat catcat ocelotocelot camelcamel

Useful Commands

$$ tartar cvfcvf playground.tarplayground.tar playgroundplayground playground/playground/ playground/documents/playground/documents/ playground/mystuff/playground/mystuff/ playground/animals/playground/animals/ playground/animals/mammals/playground/animals/mammals/ playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt playground/animals/mammals/badger.txtplayground/animals/mammals/badger.txt playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txt playground/animals/reptiles/playground/animals/reptiles/ playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt playground/science/playground/science/ $$ lsls playgroundplayground playground.tarplayground.tar

Useful Commands

$$ tartar cvfcvf playground.tarplayground.tar playgroundplayground playground/playground/ playground/documents/playground/documents/ playground/mystuff/playground/mystuff/ playground/animals/playground/animals/ playground/animals/mammals/playground/animals/mammals/ playground/animals/mammals/super_mellivorinae.txtplayground/animals/mammals/super_mellivorinae.txt“Tape ARchive” playground/animals/mammals/badger.txtplayground/animals/mammals/badger.txt playground/animals/mammals/porcupine.txtplayground/animals/mammals/porcupine.txtCombine all files (and directories) into playground/animals/reptiles/playground/animals/reptiles/ one archive file. Useful for sharing playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txtdata, archiving etc. playground/science/playground/science/ $$ lsls Use: playgroundplayground playground.tarplayground.tar tar xvf playground.tar

to re-extract.

Redirection

$$ rmrm super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ cdcd playground/animals/mammals/playground/animals/mammals/ $$ catcat badger.txtbadger.txt >> another_badger.txtanother_badger.txt $$ lsls another_badger.txtanother_badger.txt badger.txtbadger.txt“ R eporcupine.txtMporcupine.txtove” $$ catcat >> list_of_mammals.txtlist_of_mammals.txt batbat Delete a file. THERE IS NO UNDO!!! catcat ocelotocelot Add -r option to recursively remove all camelcamel files in a directory. ^D^D $$ catcat list_of_mammals.txtlist_of_mammals.txt THERE IS NO UNDO!!!!!!!!!!!!! batbat catcat ocelotocelot camelcamel

Redirection

$$ rmrm super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ cdcd playground/animals/mammals/playground/animals/mammals/ $$ catcat badger.txtbadger.txt >> another_badger.txtanother_badger.txt $$ lsls another_badger.txtanother_badger.txt badger.txtbadger.txt porcupine.txtporcupine.txt $$ catcat >> list_of_mammals.txtlist_of_mammals.txt batbat catcat Redirection ocelotocelot camelcamel “>” sends output to named file instead ^D^D of to the terminal. So, this was a way $$ catcat list_of_mammals.txtlist_of_mammals.txt to make a copy of our file. batbat catcat ocelotocelot camelcamel

Redirection

$$ rmrm super_mellivorinae.txtsuper_mellivorinae.txt $$ lsls badger.txtbadger.txt porcupine.txtporcupine.txt $$ cdcd playground/animals/mammals/playground/animals/mammals/ $$ catcat badger.txtbadger.txt >> another_badger.txtanother_badger.txt $$ lsls another_badger.txtanother_badger.txt badger.txtbadger.txt porcupine.txtporcupine.txt $$ catcat >> list_of_mammals.txtlist_of_mammals.txt batbat catcat ocelotocelot camelcamel ^D^D Redirection $$ catcat list_of_mammals.txtlist_of_mammals.txt batbat No input file given….. Terminal waits for catcat you to type input. Whatever you type ocelotocelot goes into the file. camelcamel

Redirection

$$ echoecho "More"More badgerbadger stuffstuff herehere later."later." >>>> another_badger.txtanother_badger.txt $$ catcat badger.txtbadger.txt ...... MoreMore badgerbadger stuffstuff toto gogo herehere later.later. $$ diffdiff badger.txtbadger.txt another_badger.txtanother_badger.txt 7a87a8 >> MoreMore badgerbadger stuffstuff toto gogo herehere later.later.

Redirection

$$ echoecho "More"More badgerbadger stuffstuff herehere later."later." >>>> another_badger.txtanother_badger.txt $$ catcat badger.txtbadger.txt ...... MoreMore badgerbadger stuffstuff toto gogo herehere later.later. $$ diffdiff badger.txtbadger.txt another_badger.txtanother_badger.txt 7a87a8 Append >> MoreMore badgerbadger stuffstuff toto gogo herehere later.later. Like “>”, but appends instead of over-writing.

Redirection

“DIFFerence”

Show differences between two files.

Redirection and Pipes (and Sorting)

$$ sortsort list_of_mammals.txtlist_of_mammals.txt batbat camelcamel catcat ocelotocelot $$ sortsort << list_of_mammals.txtlist_of_mammals.txt batbat camelcamel catcat ocelotocelot $$ catcat list_of_mammals.txtlist_of_mammals.txt || sortsort batbat camelcamel catcat ocelotocelot

Redirection and Pipes (and Sorting)

$$ sortsort list_of_mammals.txtlist_of_mammals.txt batbat camelcamel catcat ocelotocelot $ sort < list_of_mammals.txt $ sort < list_of_mammals.txt “Sort” batbat camel camel Sort input into alphanumerical order. catcat ocelotocelot $$ catcat list_of_mammals.txtlist_of_mammals.txt || sortsort batbat camelcamel catcat ocelotocelot

Redirection and Pipes (and Sorting)

Variables

$$ echoecho $SHELL$SHELL /bin/bash/bin/bash $$ echoecho $USER$USER abensonabenson $$ echoecho $HOME$HOME /home/abenson/home/abenson $$ workPath=$HOME/playgroundworkPath=$HOME/playground $$ cdcd $workPath$workPath $$ pwdpwd /home/abenson/playground/home/abenson/playground

Variables

$$ echoecho $SHELL$SHELL /bin/bash/bin/bash $$ echoecho $USER$USER abensonabenson Environment Variables $$ echoecho $HOME$HOME /home/abenson/home/abenson “$” means replace following with the $$ workPath=$HOME/playgroundworkPath=$HOME/playgroundvalue of the named variable. $$ cdcd $workPath$workPath $$ pwdpwd The shell sets up many environment /home/abenson/playground/home/abenson/playgroundvariables, such as those shown.

Variables

Define your own variables and then use them in the command line.

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z $$ jobsjobs $$ fgfg $$ ^Z^Z $$ bgbg $$ jobsjobs

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 Do Nothing….. $$ ^Z^Z $$ jobsjobs sleep just waits for the given number $$ fgfg of seconds. $$ ^Z^Z $$ bgbg $$ jobsjobs

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z Cancel [1]+[1]+ StoppedStopped sleepsleep 3030 $$ jobsjobs ^C cancels the running command [1]+[1]+ StoppedStopped sleepsleep 3030 $$ fgfg $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ bgbg [1]+[1]+ sleepsleep 3030 && $$ jobsjobs [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && [2][2] 2119421194

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 Suspend $$ jobsjobs [1]+[1]+ StoppedStopped sleepsleep 3030 suspends the running command $$ fgfg ^Z $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ bgbg [1]+[1]+ sleepsleep 3030 && $$ jobsjobs [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && [2][2] 2119421194

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ jobsjobs [1]+[1]+ StoppedStopped sleepsleep 3030 $$ fgfg Jobs $$ sleepsleep 3030 $$ ^Z^Z Shows a list of jobs running or [1]+[1]+ StoppedStopped suspended sleepsleep 3030 $$ bgbg [1]+[1]+ sleepsleep 3030 && $$ jobsjobs [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && [2][2] 2119421194

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ jobsjobs [1]+[1]+ StoppedStopped sleepsleep 3030 $$ fgfg $$ sleepsleep 3030 $$ ^Z^Z “ForeGround” [1]+[1]+ StoppedStopped sleepsleep 3030 $$ bgbg Bring the last suspended job back into [1]+[1]+ sleepsleep 3030 && the foregound (i.e. start running again). $$ jobsjobs [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && [2][2] 2119421194

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ jobsjobs [1]+[1]+ StoppedStopped sleepsleep 3030 $$ fgfg $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ bgbg [1]+[1]+ sleepsleep 3030 && $$ jobsjobs “BackGround” [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && Run the last suspended job in the [2][2] 2119421194 background.

Background Processes

$$ sleepsleep 3030 $$ ^C^C $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ jobsjobs [1]+[1]+ StoppedStopped sleepsleep 3030 $$ fgfg $$ sleepsleep 3030 $$ ^Z^Z [1]+[1]+ StoppedStopped sleepsleep 3030 $$ bgbg [1]+[1]+ sleepsleep 3030 && $$ jobsjobs “&” [1]+[1]+ RunningRunning sleepsleep 3030 && $$ sleepsleep 3030 && Start the command in the background. [2][2] 2119421194

Network and Remote Connections

$$ hostnamehostname dhcp225.obs.carnegiescience.edudhcp225.obs.carnegiescience.edu $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] hostnamehostname obs-ssh.ad.ciw.eduobs-ssh.ad.ciw.edu testuser@miestestuser@mies ~]~] exitexit ConnectionConnection toto mies.stanford.edumies.stanford.edu closed.closed. $$ cdcd animals/mammalsanimals/mammals $$ scpscp badger.txtbadger.txt [email protected]:[email protected]:myname.txt badger.txtbadger.txt 100%100% 19441944 1.9KB/s1.9KB/s 00:0000:00 $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] lsls badger.txtbadger.txt testuser@miestestuser@mies ~]~] rmrm myname.txtmyname.txt testuser@miestestuser@mies ~]~] exitexit ConnectionConnection toto mies.stanford.edumies.stanford.edu closed.closed.

Network and Remote Connections

$$ hostnamehostname dhcp225.obs.carnegiescience.edudhcp225.obs.carnegiescience.edu $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] hostnamehostname obs-ssh.ad.ciw.eduobs-ssh.ad.ciw.edu testuser@miestestuser@mies ~]~] exitexit “Secure SHell” ConnectionConnection toto ssh.obs.carnegiescience.edussh.obs.carnegiescience.edu closed.closed. $$ cdcd animals/mammalsanimals/mammals Open a shell on a remote server. $$ scpscp badger.txtbadger.txt [email protected]:[email protected]: badger.txtbadger.txt 100%100% 19441944 Password1.9KB/s1.9KB/s is: HvtTc6Bw00:0000:00 $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] lsls badger.txtbadger.txt testuser@miestestuser@mies ~]~] rmrm badger.txtbadger.txt testuser@miestestuser@mies ~]~] exitexit ConnectionConnection toto ssh.obs.carnegiescience.edussh.obs.carnegiescience.edu closed.closed.

Network and Remote Connections

$$ hostnamehostname dhcp225.obs.carnegiescience.edudhcp225.obs.carnegiescience.edu $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] hostnamehostname obs-ssh.ad.ciw.eduobs-ssh.ad.ciw.edu testuser@miestestuser@mies ~]~] exitexit ConnectionConnection toto ssh.obs.carnegiescience.edussh.obs.carnegiescience.edu closed.closed. $$ cdcd animals/mammalsanimals/mammals $$ scpscp badger.txtbadger.txt [email protected]:[email protected]: badger.txtbadger.txt 100%100% 19441944 1.9KB/s1.9KB/s 00:0000:00 $$ sshssh [email protected]@mies.stanford.edu LastLast login:login: ThuThu JunJun 22 14:03:0114:03:01 20162016 fromfrom ociw.eduociw.edu testuser@miestestuser@mies ~]~] lsls “Secure CoPy” badger.txtbadger.txt testuser@miestestuser@mies ~]~] rmrm badger.txtbadger.txtCopy a file to a remote server. Or from testuser@miestestuser@mies ~]~] exitexit remote server to your laptop. ConnectionConnection toto ssh.obs.carnegiescience.edussh.obs.carnegiescience.edu closed.closed.

Network and Remote Connections

$$ wgetwget http://bit.ly/1TXIZSJhttp://bit.ly/1TXIZSJ -O-O playground1.tarplayground1.tar

wget

Download a file from a URL. Useful for downloading big datasets on a remote server.

Scripts

#!/bin/sh#!/bin/sh

echoecho ThisThis isis aa script….script…. echoecho HelloHello useruser $USER$USER echoecho HereHere areare allall thethe filesfiles II cancan find…find… findfind .. -type-type ff exitexit

Scripts

$$ cdcd ~/playground~/playground $$ ./script.sh./script.sh ThisThis isis aa script...script... HelloHello useruser abensonabenson HereHere areare allall thethe filesfiles II cancan find…find… ./script.sh./script.sh ./animals/mammals/badger.txt./animals/mammals/badger.txt ./animals/mammals/porcupine.txt./animals/mammals/porcupine.txt ./animals/reptiles/caiman.txt./animals/reptiles/caiman.txt

Scripts: .bashrc

● The script in ~/.bashrc gets run every time you log in ● Use it to configure the environment the way you want it to be ● For example, you could add an alias:

$$ aliasalias up='cdup='cd ..'..' $$ cdcd ~/playground/animals~/playground/animals $$ pwdpwd /home/abenson/playground/animals/home/abenson/playground/animals $$ upup $$ pwdpwd /home/abenson/playground/home/abenson/playground

Bonus: Text Editing with EMACS

● There are many text editors in Unix ● Use whichever you prefer ● One option available everywhere is EMACS

$$ emacsemacs playground/animals/reptiles/caiman.txtplayground/animals/reptiles/caiman.txt && [1][1] 2957529575

Bonus: Text Editing with EMACS

Open file ^X^F Cut ^W

Save file Paste ^X^S ^Y

Close file ^X^K Search forward ^S

Search backward ^R Exit EMACS ^X^C