Permissions

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2.0.0.3.2 Introduction to the Shell Session 2

• Permissions
• Users and groups
• Who can do what and how to control it
• Customizing your environment
• Changing the shell prompt
• Aliases
• Environment variables
• Saving customizations
• Pipes and redirection
• Controlling input and output
• Running a series of commands
• Running programs on the command line

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UNIX Users and Groups

• Every file/directory belongs to a user and a
  group
• People logged on to UNIX systems are users
• Check who you are logged on as with
• Change who you are logged on as with

whoami
su
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UNIX Users and Groups

• Check which groups you belong to with
• See what user and group a file belongs to with ls
  l or stat (as in 2.0.0.3.1)

groups
Group
User
Group users Every user at GSC belongs to the
group users, and this is the default group
ownership for any file created.
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UNIX Users and Groups chgrp

• Users (except root) cannot change which user owns
  a file
• Change the group that a file (or directory)
  belongs to with
• -R change recursively (all subdirectories and
  files)

chgrp
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The Permissions System reading, writing, and
executing

• Permissions refer to the type of access that
  users have to files
• Allows files to be private, public, read-only,
  etc.
• There are three types of access possible
• Read (ability to see the contents of a file, or
  list the contents of a directory)
• Write (ability to modify or delete a file, or
  create files in a directory)
• Execute (ability to run the file as a program
  eg. Perl scripts need to be executable or enter
  a directory)
• Permissions are set individually for
• User
• Group
• All users

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The Permissions System reading, writing, and
executing

• Read, write, and execute permissions for user,
  group, and all users are specified as r, w
  and x (if the permission is given) or - (if
  the permission is denied)

For all users
For group
For user
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Changing Permissions chmod

• If you own a file, change permissions using
• Specify

chmod
chmod ugoa-rwx
Other options -R apply recursively
Who to modify permissions for u user g
group o other (all users) a all (u,g, and o)
Whether to give or take permission give -
take away these are the only permissions
What permission to modify r read w write x
execute
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Changing Permissions chmod examples

• Make a file private (only you can see it)
  -rw-------
• chmod og-rw or chmod og
• Make a file public (everyone can modify it)
  -rw-rw-rw-
• chmod arw
• Make a directory private (only you can view its
  contents) drwx------
• chmod og-rwx or chmod og
• Make a directory usable by anyone (anyone can add
  files to it) drwxrwxrwx
• chmod arwx
• Make a file executable -rwxr-xr-x
• chmod ax

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Changing Permissions chmod and umask

• You can also use a set of numbers to set
  permissions

• Specify default permissions for all newly created
  files with

umask
http//www.cs.ualberta.ca/doc/UNIX/novice-unix-doc
/permissions.html
eg. umask 022 -rw-r--r (files)
-rwxr-xr-x (directories)
eg. chmod 644 -rw-r--r--
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Other file attributes chattr

• In addition to specifying permissions, other file
  attributes can be set with
• eg. set the file so it cannot be deleted, so its
  access time is not updated, or so that it is
  stored in compressed form.

chattr
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Customizing your Environment Environment
variables

• Environment variables store information about how
  your shell should look and behave, where to find
  things, particular program settings, etc. They
  are used by programs running in the shell.
• See what environment variables are currently set
  with
• Set environment variables with
• ltVARIABLEgtnew value
• Delete environment variables with

printenv
unset
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Setting the Prompt PS1

• Get colourful! To specify colour, bracket the
  colour code between a \e (or \033) and an
  m
• 30 Black
• 31 Red
• 32 Green
• 33 Yellow
• 34 Dark blue
• 35 Purple
• 36 Light blue
• 37 White

• The environment variable PS1 stores what is
  displayed at the prompt
• Use special characters
• \d date
• \t and \_at_ time
• \h hostname
• \u username
• \w current directory

Word wrapping isnt working! When modifying
colours in PS1, surround the color specifications
with \ and \ to tell the shell that text
doesnt take up any space on the prompt.
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Specifying Where to Look for Programs PATH

• The PATH variable stores a list of directories
  where the shell and other processes should look
  for programs
• Each entry is separated by
• Start your path with . to run scripts without
  specifying ./

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Specifying Where to Look for Directories CDPATH

• CDPATH is like PATH, but instead of specifying
  where to look for programs, it specifies where to
  look for directories
• Be careful, it can be dangerous. always put .
  first!

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Other Environment Variables

• HISTSIZE specifies the number of commands to keep
  in the history
• PRINTER specifies the printer name
• PWD stores the current directory (used by pwd)
• OLDPWD stores the previous directory (used by cd
  )
• LS_COLORS specifies colours to display different
  file/directory types as (used by ls color)
• Various programs require other environment
  variables
• BLAST
• SRS
• Java
• Perl
• Etc.

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Defining Commands aliases

• An alias is a short form of a command that can
  save on typing
• View and assign aliases with
• To use the normal command, not the alias, use
• \ltcommandgt
• eg. \ls lists with no colour etc.

alias
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Customizing your Environment Configuration at
startup

• Customizations are lost when you logout
• To save them, put them in one of your
  configuration files
• .bash_profile (/home/ltusergt/.bash_profile) is run
  every time you log on
• .bashrc (/home/ltusergt/.bashrc) is run every time
  you open a shell other than the login shell
• export the variables so you can see and access
  them

• Oops!
• Careful. If you do something wrong (like make
  text white on white) it can be difficult to fix
• Test everything before putting it in .bashrc or
  .bash_profile
• Keep an extra terminal window that was opened
  BEFORE you made the changes, so you can use that
  terminal to fix mistakes

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Input, Output, and Error

• Data can be transferred (eg. between commands) in
  the shell using three streams
• Standard input (STDIN in Perl) Input to a
  process, by default from the keyboard
• Standard output (STDOUT in Perl) Output from a
  process, by default to the terminal window
• Standard error (STDERR in Perl) Another stream
  of output from a process, by default to the
  terminal window
• eg.
• cat takes a file or text from the terminal as
  standard input, writes the file contents to
  standard output (the terminal)
• Error messages from commands are written to
  standard error
• Perl scripts by default write to standard output

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Redirecting Input, Output, and Error gt, lt, gtgt,
2gt, gt
append stdout

• Redirect standard input to a file with lt
• Redirect standard output to a file with gt or 1gt
• Redirect standard error to a file with 2gt
• Redirect BOTH standard output and error to a file
  with gt
• Redirect standard output to append to a file with
  gtgt

stdout
stderr
/dev/null A useful file to redirect to is
/dev/null anything redirected here just
disappears. Good for programs that produce a lot
of verbose messages that you dont need to see or
keep.
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Example Perl output

• It is good practice to separate real output
  from error messages when running Perl scripts

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Running a Series of Commands pipes

• To put the standard output of one command
  directly into the standard input of another, use
  a pipe (on the keyboard above the \)
• You can do this as many times as you like on one
  line especially useful for command line tools
  like grep, cut, sort, wc, etc. (see session
  2.0.0.3.3)

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Running Programs on the Command Line

• With correctly set environment variables and
  ability to redirect output, you will find it much
  easier to run command-line programs (eg. BLAST)
• To check where a program is installed, use
• If the command is in your PATH, the shell will
  tell you where it is
• Important to check when there is more than one
  version of the program installed (eg. Perl at
  GSC!)

which
Getting help Many programs will give short help
messages when run without any parameters (eg.
perl, blastall). Otherwise, try option h or
--help. To check the program version, try
--version.
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2.0.0.3.2 Introduction to the Shell Session 2

• Now you know.
• How to see and set permissions
• How to customize your environment, and save
  customizations for future sessions
• How to control input and output, and run a series
  of commands
• Next youll learn.
• Job control
• Command line goodies (really useful tools)
• Command line Perl

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2.0.0.3.2 Further Readings

• Permissions
• Linux Cookbook Ch. 7
• Learning the UNIX Operating System Ch. 3.3
• Customizing the shell
• Linux Cookbook Ch. 4.6
• Learning the UNIX Operating System Ch. 3.6
• PS1 http//www-106.ibm.com/developerworks/linux/l
  ibrary/l-tip-prompt/
• Redirecting input and output
• Linux Cookbook Ch. 4.2
• Learning the UNIX Operating System Ch. 5