Helpful commands

A cheatsheet of helpful Bash commands.

Overview #

This page introduces commands that are completely safe and purely display information that may be used by users to get help or explore the environment of the CCB cluster

echo #

The echo command can be used to print a message or the value of a variable.

For instance:

echo 'Hello, world!'

man #

The man <page> command can be used to print the reference manual page <page>.

In many cases, <page> is the name of the command that you wish to execute.

For instance, the reference manual page for the command pwd can be displayed as follows:

man pwd

Incidentally, the reference manual page for the command man is opened as follows:

man man

The ability to access, read, and understand manual pages is one of the first essential skills to develop as a Bash user.

type #

The type <name> command can be used to identify how <name> would be interpreted if used as a command.

type pwd
type less

Identifying commands that are Bash built-in or additional command from third-party software can be helpful to understand and investigate bugs and unexpected behaviours.

which #

The which <program> command can be used to display the full path to the command <program>.

which man

groups #

The groups command can be used to print the user groups that a user belongs to.

Alone, the groups command display the list of user groups that current user belongs to.

groups

The groups <username> command can also be given a username, in which case it will display the list of user groups that particular user belongs to.

realpath #

The realpath command can be used to resolve the absolute file path to a specific file or directory in the filesystem.

In many cases, files and directories may be referred to through any valid path. However, in some cases, it may be necessary to identify and use the ‘real’ path to a file or directory, meaning the unambiguous absolute path to that file from the root directory.

realpath file1.txt

wc #

The wc <file> command can be used to count the number of lines, words, or bytes in files.

Most commonly, the wc command is used with the option -l to specifically focus on the number of lines in a given file. This is particularly useful for bioinformatics file formats where results are reported one per line.

For instance, the SAM file format reports alignments of sequences to a reference genome, one per line, meaning that the number of lines indicates the total number of alignments.

wc -l file1.txt 

Commonly used options for the wc command: