• Is a Unix shell:
  • GNU implementation of the Bourne shell (sh) from 1979
  • can be seen as interface between the user and the operating system (OS)
  • users interact with the shell using a terminal emulator (e.g. direct or via ssh)
  • interactive command language and a scripting language
• Other sh like shells:
  • zsh, ksh, ash

• filename wildcarding
  *.{png,jpg}
• piping
  • cmd1 | cmd2 | ... | cmdN
• here documents
  cat << EOF
line1
line2
EOF
• command substitution
  gzip `grep ".fastq" filelist.txt`
  or
  gzip $(grep ".fastq" filelist.txt)

• variables
  

  VAR="foo"; echo $VAR

• control structures for condition-testing
  

  if [ $FOO == $BAR ]; then ... fi

• iteration (loops)

  for ((i=1; i<=10; i++)); do echo Hello $i; done
  or
  i=1; while [ $i -le 10 ]; do echo Hello $i; ((i++)); done

Config files contain commands that are executed when loaded

Important and useful settings

• $PATH variable
  • ~/.bash_profile
  • environment variable
  • specifies a set of directories where executable programs are located
  • program will be run from the first directory it is found in

e.g. 
$ echo $PATH
$ /usr/local/bin:/usr/bin:/bin:/usr/sbin:/home/gringo/bin:/opt/pycharm/bin

Important and useful settings

• $JAVA_HOME
  • directory in which JRE is installed
• $LD_LIBRARY_PATH
  • path to system and program libraries
• $HISTSIZE variable
  • specifies how many commands are saved in history
    $ echo $HISTSIZE
$ 1000
• $EDITOR
  • sets the default text editor (e.g. nano, mcedit)

variables are set w/o leading $, e.g.
$ JAVA_HOME=/usr/java/jdk/1.12/

Unix shells allow aliasing commands, that is replacing a command by an arbitrary string.

Used to abbreviate commands or add default options to a command, e.g.:

• alias l='ls -la'
• alias tsv='column -t -s$'\''\t'\'

Hint: to persist your aliases set them in ~/.bash_profile

To remove an alias use:

• unalias <alias>

To alias a command that should get an argument passed we can use bash functions()

e.g.

mkcd() {                                                                                                                                                                                                
    local d="$1"                                                                                                                                                                                                  
    mkdir -p $d
    cd $d
}

Would use the first argument to create directory and directly change into it

$ mkcd /tmp/a/b/c
$ pwd
$ /tmp/a/b/c

Most UNIX programs have a manual page to document the options for the command

• manual page can be accessed using
  $ man <program name>
  e.g. 
  $ man cat
• will display detailed usage, options and examples for cat
• man pages usually have the following sections:
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • EXAMPLES
  • AUTHOR, REPORTING BUGS, COPYRIGHT, SEE ALSO