Hofmockel.org

Linux Tutorial

One needs to know several things to use a new operating system.
Among these are how to create files, move files, copy files, delete
files, check your mail, use a web browser, find programs and
applications, and change the appearance of your working environment.
This page gives an overview of Linux basics for those who are
unfamiliar with them. For an extensive list of other Linux commands,
try the O'Reilley Open Source Linux development website.

* Listing Directory Contents
* Locations of Files and Directories
* Viewing Files
* Creating and Editing Files
* Moving Files
* Copying Files
* Deleting Files
* Creating Directories
* Changing Directories
* Deleting Directories
* Viewing PDF Files
* Getting Help
* ssh
* Copying files between machines

Listing Directory Contents

To list all directories and files within a current directory, type:

ls

To list a detailed list of all directories and files sorted by creation date, type:

ls -lrt

Locations of Files and Directories

To work with a file or directory, it is important to tell Linux
where to find it. There are several ways to tell Linux where to look:

./ = the current directory
../ = the parent directory of ./ (one directory up)
/ = the root directory (top directory)

When no location is specified, Linux assumes we mean "./". So we can
copy "fileX" from the current directory to its parent directory using
either:
cp /whole/path/from/root/directory/fileX ../

or:
cp ./fileX ../

or:
cp fileX ../

Viewing Files

There are many ways to view a text file. For viewing and editing,
see the section below on text editors. One way for simple viewing is to
type:

less

This displays as much of the file as can fit onto the screen. To
scroll up and down within the document, use the arrow keys. Hitting the
space bar will bring a new screen-full of information.

To search forward in the file for a given pattern, press:

/pattern

To exit less, press:

q

Creating and Editing Files

There are several text editors that create plain text files. We have
emacs and vi available from the terminals. Unless you are already
familiar with vi, we strongly recommend that you use emacs. We strongly
recommend you study the emacs tutorial, which you can easily start in
any emacs session. To open and edit a file in emacs, simply type

emacs myfile

To create and edit a new file, type

emacs newfile

To edit a file in emacs and still be able to use the command prompt, type

emacs myfile &

If you forgot to type the "&" and you want to return to the command prompt mode, type

Control-Z

This command will suspend the emacs application, but will not kill it. Then type:

bg

to have emacs working in the background.

***User home directories are set at a maximum storage space of 3
gigabytes. Should you exceed your storage space, you will be warned
that you are at your maximum storage space. Contact the Workshop
computer staff before the grace period on this expires and anything of
yours is possibly lost.***

Moving Files

Because of the way files are accessed in UNIX/Linux, moving a file is the same as renaming it. The command mv works like:
mv file1 file2

For example:

mv fileformats.html index.html

takes fileformats.html and renames it index.html.
Files can be moved from one location to another:

mv location/file1 location/file2

For example:

mv /home/mwaring/to-do-list /home/mwaring/Tasks/

This command moves the file to-do-list from /home/mwaring/ to
/home/mwaring/Tasks/. To move a file and also rename it, specify a name
after the second location. For example:
mv /home/mwaring/more-stuff /home/mwaring/Tasks/additional-tasks

Copying Files

To copy a file using a terminal, use
cp

For example:

cp template.html course-schedule.html

This makes a new file that contains the same information as the
first file with the name indicated. In the example above, cp takes the
contents of template.html and makes a file called course-schedule.html
that contains all the information in template.html.

cp can also be used to copy a file from one directory to another. For example:

cp /home/tmp/mbl.color.logo.jpg /home/mwaring/images/MBL.jpg

This command will take MBL.color.logo.jpg in /home/tmp and copy it
to /home/mwaring/images. It names the copy MBL.jpg. If a name is not
specified for the file, a copy with the same name as the original is
made. For example:

cp /home/tmp/mbl.color.logo.jpg /home/mwaring/images

To copy an entire directory, use the -R flag.

cp -R dir-to-copy/ new-dir/

For example:

cp -R /home/tmp/images/ /home/mwaring/temp-images

copies the directory in /home/tmp called images into the temp-images
directory in /home/mwaring. Note: on some computers, cp -R does not
copy dot-files (files that start with '.', for example .bashrc).

You may run into trouble copying files from or to directories which you do not have permission to read or execute.

Removing Files

rm is the command to remove a file. There are flags (options) that can be used with rm. To delete a file, type:

rm filename

For example, to delete a file called coi.nex, type:

rm coi.nex

A prompt will ask if you really want to delete it. If so, type:

y

To delete a file from a different directory, supply rm with the pathname. For example:

rm /home/mwaring/coi.nex

Creating Directories

To create a new directory, type:

mkdir directory1

This will create a directory called directory1.

Changing Directories

To view the pathway of the current directory, type:

pwd

This will show output such as

/home/mwaring/directory1

To go "up" one directory (in this example, to go from directory1 to mwaring), type:

cd ..

To go "down" one directory (in this example, to go from mwaring to directory1), type:

cd directory1

To go "back" to your home directory, type:

cd

Deleting Directories

To delete a directory, type:

rm -r directory1

This will remove the directory and all the files in it so use this command carefully.

Viewing PDF files

PDF files can be accessed by either downloading and saving or
reading files directly. To view files that have been downloaded, go to
the terminal window and type:

acroread file1

This will open the pdf file in acrobat reader.

Getting Help

While the workshop is in session, one of your best sources of help are the teaching assistants and support staff.

This page will still be accessible after the course, but contains
help on only a few basic UNIX commands. Some material may not apply to
your home systems. On most systems, typing

man command

invokes information about commands.

For example, to learn how cp works, type:

man cp

To exit the man page, hit:

q

Note: man pages are often a bit obtuse, but are worth reading nevertheless.

ssh

ssh is a program to connect to another computer. For Linux and Mac OS X, there are two ways of using ssh from a terminal:

ssh user@computer

or

ssh computer -l user

For example:

ssh mwaring@gcg.workshop.priv

or

ssh gcg.workshop.priv -l mwaring

You will then be asked for your password.

If you are using a notebook computer and it does not already have an
ssh client program, you can get one for free. For MacOS 9, visit Nifty
Telnet-SSH and download the client. Windows users can download Putty, a
free ssh client.

Note: Your home directory (and all of /home) is available for you on every machine in the lab.

Copying Files between Machines (File Transfer)

Some of you may be familiar with ftp (File Transfer Protocol). We do
not have ftp here because it is a relatively insecure method of
transferring files between computers. To transfer files between
machines, you need to use:

scp

This command works very similarly to cp, except that the files you are copying reside on different machines.

To copy a file from a remote computer to the computer you are working at, you type:

scp user@remote-computer:/remote/path/remote-file /local/path/local-file

You will then be prompted for the user's password on the remote
computer. After you enter it, the file will be copied. For example:

scp molly@bigbox.university.edu:/home/molly/Info/info /home/mwaring/facts

If I am working on nixon (for example), this command will copy the
file called info that lives on bigbox.university.edu at
/home/molly/Info to /home/mwaring on nixon and will name it 'facts'.
For those of you familiar with ftp, this is like 'get remote-file
local-file'. Note: if you do not specify a local name, scp will name
the file the same name as the remote file.

To copy a local file onto a remote computer, you type:

scp /local/path/local-file user@remote-computer:/remote/path/remote-file

For those of you familiar with ftp, this is like 'put local-file
remote-file'.Note: As with cp, you need to have read/execute
permissions on the two files. Also, you should only specify one
computer name (either the local host or the remote host).

As with the cp command, you can specify the -r flag to recursively copy entire directories.

Note: This does not work with Windows machines. scp works only between UNIX/Linux machines.

Note 2: You will never need to scp files between computers in the
Workshop: your home directory is available on all of the computers. You
only need to use scp to exchange data with computers outside of the
Workshop.

ref: http://workshop.molecularevolution.org/resources/computing.php#mv