6.1
Introduction
Most computer users today are familiar with the graphical user interphase (GUI), however,
it has been said that “graphical user interfaces make easy tasks easy, while the command
line interfaces (CLI) make difficult tasks possible.” That is reason enough to spend more
time with the CLI, as we often have to deal with more difficult issues within NGS data
analysis.
When we speak of the command line interface, we actually are referring to the shell,
which is a program that takes keyboard commands and passes them to the operating system
to carry out. Most Linux distributions supply a shell program from the GNU Project called
Bash (bourne-again shell), which is a replacement for sh (the original Unix shell program).
Bioinformatics is a lot about manipulating text files, thus the usage of the command line
interpreter (CLI) or shell is an essential tool. CLI or shell is a program that parses and
executes commands from the user in the terminal. A common command line interpreter
is Bash.
6.2
The Linux/Unix File System
The purpose of this chapter is to introduce you to how files and directories are handled in
Linux/Unix and how to navigate and manipulate your file system from the command line
tool (terminal). If you are opening your terminal (Unix: Applications! Utilities! doubleclick Terminal; Linux: Strg + Alt + T or search in Applications/Accessories ! Terminal),
you are placed in your “home” directory, which is than your “present working directory”
(pwd). In your home or another present working directory, you can create files and
subdirectories. The commands that you issue in the terminal at the Unix prompt ($) relate
to the files and folders and resources available from your present working directory.
Understanding the Linux/Unix file system also enables you to use and refer to resources
outside of your current working directory. The Linux/Unix file system is depicted in
Fig. 6.1.
All files are organized in a tree-like structure starting at the root folder /.
Purpose of each of directory:
• usr/bin: Most commands and executable files.
• /dev: Device entries for disks, printers, pseudo-terminals, etc.
• /etc: Critical startup and configuration files.
• /sbin: Commands needed for minimal system operability.
• /home: Default home directories for users.
• /var: System specific data and configuration files.
• /tmp: Temporary files that may disappear between reboots.
• /opt: Optional software packages (not consistently used).
72
M. Kappelmann-Fenzl
Introduction
Most computer users today are familiar with the graphical user interphase (GUI), however,
it has been said that “graphical user interfaces make easy tasks easy, while the command
line interfaces (CLI) make difficult tasks possible.” That is reason enough to spend more
time with the CLI, as we often have to deal with more difficult issues within NGS data
analysis.
When we speak of the command line interface, we actually are referring to the shell,
which is a program that takes keyboard commands and passes them to the operating system
to carry out. Most Linux distributions supply a shell program from the GNU Project called
Bash (bourne-again shell), which is a replacement for sh (the original Unix shell program).
Bioinformatics is a lot about manipulating text files, thus the usage of the command line
interpreter (CLI) or shell is an essential tool. CLI or shell is a program that parses and
executes commands from the user in the terminal. A common command line interpreter
is Bash.
6.2
The Linux/Unix File System
The purpose of this chapter is to introduce you to how files and directories are handled in
Linux/Unix and how to navigate and manipulate your file system from the command line
tool (terminal). If you are opening your terminal (Unix: Applications! Utilities! doubleclick Terminal; Linux: Strg + Alt + T or search in Applications/Accessories ! Terminal),
you are placed in your “home” directory, which is than your “present working directory”
(pwd). In your home or another present working directory, you can create files and
subdirectories. The commands that you issue in the terminal at the Unix prompt ($) relate
to the files and folders and resources available from your present working directory.
Understanding the Linux/Unix file system also enables you to use and refer to resources
outside of your current working directory. The Linux/Unix file system is depicted in
Fig. 6.1.
All files are organized in a tree-like structure starting at the root folder /.
Purpose of each of directory:
• usr/bin: Most commands and executable files.
• /dev: Device entries for disks, printers, pseudo-terminals, etc.
• /etc: Critical startup and configuration files.
• /sbin: Commands needed for minimal system operability.
• /home: Default home directories for users.
• /var: System specific data and configuration files.
• /tmp: Temporary files that may disappear between reboots.
• /opt: Optional software packages (not consistently used).
72
M. Kappelmann-Fenzl