What is a shell? • a program to interact with a computer • a program that runs other programs • especially useful for command line programs • not a GUI/windows system • many flavors, bash is the most popular Why use a shell? • your favorite program only has a command line interface. This happens often if you work remotely, e.g. by dialing into department machines. – ex: writing a quick R script on a remote machine – $ ssh [email protected] – $ nano mydocument.txt • automation of mundane tasks in file system and os interactions Secure shell • ssh # make a secure shell connection • scp # copy a file with secure shell Navigating the file system • $ pwd # print working directory • $ ls # list files and directories • $ ls -tahlF # list files and directories in a list (l), including hidden files (a) with human readable file sizes (h), in chronological order (t), with slashes after directories (F) • $ cd Documents # change working directory to Documents/ • $ mkdir new_paper # make a new directory inside the Documents folder • $ nano draft.txt # nano is a super lightweight text editor • $ rm draft.txt # delete the text file (BE CAREFUL WITH THE RM COMMAND) • $ rmdir new_paper # delete an empty directory • $ cp # copy a file • $ mv # move a file 1 • $ grep # find lines in files – $ grep -n stats draft.txt • $ find # find files – $ find . -type d – $ find . -maxdepth 1 -type f – $ find . -empty – $ find . -name ‘*.md’ • generic wildcards with back quotes – $ wc -l find . -name ’*.md’ • grep and find together – $ grep SNP find . -name ’*.md’ – $ grep ‘\vec{q}’ find . -name ’*.tex’ to find some expression in your .tex files. Note the quotation marks ‘’ and ‘ ‘ are different. Useful odds and ends • . # shortcut for the current working directory • .. # shortcut for the parent directory • - # shortcut for the previous directory • $ clear # clears the page • $ touch # creates a file without running any other program • $ wc # counts the lines, words, and characters in a file • redirecting output to a file – $ wc -l draft.txt > filelengths.txt # find the number of lines in draft.txt and save in filelengths.txt – $ cat filelengths.txt # show the content of filelengths.txt – redirecting with >> appends instead of overwriting. • piping output to another command – $ wc -l *.txt | head -1 # finds the line length of all .txt files and sends the result to the ‘head’ command, which prints only the first line – $ wc -l *.txt | sort | head -1 2 • $ tree - tree needs to be installed (apt-get or brew both work). It displays files/directories in a tree structure, and can accept most of the options you can pass to ls. • top - displays system usage information • htop - displays system usage information with some ASCII graphics for processor usage. • screen # for persistent SSH sessions with better control • nohup Aliases and shell scripting • $alias lm=“ls -tahlF” – not permanent. – to make a permanent alias, save it in .bashrc or .bash_aliases • $ set • $ echo $PATH • $ echo $HOME • looping – $ for file in *.md; do head -1 $file; done Running shell commands in other programs • R “system” – system(‘echo $HOME’) – x = system(‘echo $HOME’, intern=TRUE) – print(x) • IPython “!” – basic commands are native (pwd, ls, cd) – x = !echo $HOME – print x Password-free SSH • $ ssh-keygen • $ [enter a passphrase if so desired] 3.