Files and permissions

A brief introduction to working with files and managing permissions on the CCB cluster.

Example scenario #

In this page, examples refer to the layout of files and directories illustrated in the schematic below.

Absolute and relative paths #

Absolute file paths start from the ‘root’ directory, represented by the / symbol.

For instance, in the example scenario illustrated above, the following file and directory paths are valid:

/
/bin
/bin/bash
/usr/local
/usr/local/bin

Relative file paths describe paths relative to the working directory. As such, they start with any valid character other than /, either referring to the name of a sub-directory, or using the .. shortcut referring to the parent directory.

For instance, in the illustration above, the following file and directory paths are valid, relative to the working directory /usr:

bin
include
local
local/bin
../bin
../bin/bash
../etc/crontab

Both absolute and relative paths can be used in Bash commands.

For instance:

cd /usr/local/bin

Shortcuts #

• The symbol . (full stop) refers to the current directory.
• The shortcut .. (two consecutive full stop symbols) refers to the parent directory.
• The symbol ~ (tilde) refers to the home directory of the current user.
• The / symbol (forward slash) refers to the root directory of the filesystem.

The working directory #

The current working directory is always indicated in the prompt of the Linux shell.

In the example below, the prompt initially indicates the working directory to be the home directory (represented by the symbol ~, highlighted in red below). After using the cd command to change directory, the prompt then indicates the new working directory.

File permissions #

File permissions are critical to ensure that access to individual files and directories is restricted to the appropriate users.

Each file is owned by exactly one user (indicated in the the column highlighted as ‘username’ below).

Moreover, each user can belong to a number of user groups, and each file is assigned to exactly one user group (indicated in the the column highlighted as ‘usergroup’ below) that can be given its own set of permissions on that file.

File permissions can be displayed using the ls -l command. In the example below, the options -a and -F are added to display hidden files and append a symbol indicating the type of each file.

For a single file, permissions are indicated as a sequence of characters (e.g. drwxrwxr-x).

The first character is either d if the file is a directory, or - if it is a regular file.

The remaining sequence of characters is read in triplets that represent permissions for three groups of users:

• first triplet: the user who owns the file
• second triplet: the user group assigned to the file
• third triplet: every other user who is not the file owner and does not belong to the user group assigned to the file.

Each triplet is interpreted as follows:

• The character r indicates that the corresponding user(s) have read access to the file (i.e., they can open the file).
• The character w indicates that the corresponding user(s) have write access to the file (i.e., they can edit the file).
• The character x indicates that the corresponding user(s) have execute access to the file (i.e., they can run the file as a program).
• The character - indicates that the corresponding user(s) do not have the corresponding permission on that file.

For directories, the permission are better described as follows:

• The ‘read’ permission indicates the permission to list the contents of the directory.
• The ‘write’ permission indicates the permission to create or edit files in that directory.
• The ’execute’ permission indicates the permission to navigate (i.e., change directory) into that directory.

Changing file permissions #

The chmod <permissions> <file_or_directory> command can be used to modify the permissions on individual files and directories.

Most commonly, changes in file permissions are made to:

• Make script files executable.
• Make valuable files (e.g., raw sequencing data) read-only, to avoid accidentally deleting them.

File permissions can be described in two formats:

• the alphabetical notation, which is more verbose, but often easier to read and write.
• the octal notation, which is more compact, but often takes more practice to read and write.

Using alphabetical notation #

To change file permissions using the alphabetical notation, the chmod command takes two arguments:

• the permissions to modify
• the set of files and directories affected by those changes

The permissions to modify are declared using the following syntax:

• u for user, g for group, o for other
• - for removing permissions, + for adding permissions
• r for read, w for write, x for execute permission
• , for separating multiple sets of changes

For instance, the example below illustrates how the chmod command can be used to simultaneously:

• add execute permission for the user who owns the file (i.e., u+x)
• remove write permission for the user group assigned to the file (i.e., g-w)
• remove read permission for every other user (i.e., o-r)

chmod u+x,g-w,o-r file1.txt

When the same permissions are applied to multiple groups, the command may be simplified by combining the characters representing those groups together.

In the example below, read, write, and execute permissions are all removed simultaneously from both the user group and other users:

chmod go-rwx file1.txt

Using octal notation #

To change file permissions using the octal notation, the chmod command takes two arguments:

• the new set of permissions
• the set of files and directories affected by those changes

The new set of permissions are declared using the following syntax:

• a triplet of digits indicates the new permission for each of the three types of users (owner, group, other).
• a value of 4 indicates read permission
• a value of 2 indicates write permission
• a value of 1 indicates execute permission
• for each type of user, values are added together to make a digit between 0 (no permission) and 7 (all permissions).

For instance, the example below illustrates how the chmod command can be used to simultaneously:

• give read, write, and execute permission to the owner of that file
• give only read permission to the group assigned to that file
• remove all permissions to other users on that file

chmod 740 file1.txt