Fedora Core 4

Introduction

Use these instructions to install GNU/Linux and the software required for supporting a web server and MySQL database server that generates dynamic web pages using Perl or PHP. These instructions tell you how to install and configure:

• the Fedora Core 4 distribution of GNU/Linux, which includes:
  • Apache httpd 2.0.54
  • MySQL 4.1.15
  • Perl 5.8.6
  • PHP 5.0.4
• graphics, numerics, and software development packages frequently used for web development
• phpMyAdmin 2.6.4-pl3

Fedora is an open source GNU/Linux project sponsored by Red Hat. Fedora Core 4 was released on June 9, 2005.

These instructions assume you are installing Fedora Core 4 onto a PC with a 32-bit Intel or AMD processor. I have created these instructions by installing Fedora Core 4 on a Toshiba Satellite Pro laptop.

More information about Fedora Core 4 is available in the following books:

• Red Hat Fedora 4 Unleashed
• Red Hat Enterprise Linux & Fedora Core 4: The Complete Reference

falko provides instructions for The Perfect Setup—Fedora Core 4 at www.howtoforge.com.

Install and Configure Fedora Core 4

Obtain the Fedora Core 4 Installation CDs

The ISO images for the installation CDs for Fedora Core 4 can be downloaded from the Fedora Core Download Server. You need to download the following files:

• FC4-i386-disc1.iso (635M)
• FC4-i386-disc2.iso (638M)
• FC4-i386-disc3.iso (638M)
• FC4-i386-disc4.iso (630M)

Since the downloads are large, you need a high-speed Internet connection to obtain them. Even then, it will take three to four hours to download all four images.

One you have downloaded the files, you need to burn each file to a CD. I did this on my PowerBook using Apple’s Disk Utility.

The install disks are also available in the books listed above.

Install Fedora Core 4

Boot from Fedora Core Disk 1

Configure the BIOS of your computer so it will boot first from the CD drive. On my Toshiba laptop, I entered the BIOS configuration by pressing the Esc key immediately after turning on the computer. The BIOS configuration screen allowed me to direct the computer to attempt to boot first from the internal CD drive. I saved this setting and exited the configuration screen.

On my Toshiba laptop, I could also select the boot device by pressing F12 immediately after startup. The Toshiba BIOS presented a set of icons depicting the possible boot devices (diskette drive, hard drive, CD-ROM, and network). I used the arrow key to select the desired boot device, and then I pressed the Enter key.

Place Fedora Core 4 Disk 1 into the CD drive, and reboot the computer from the CD.

Choose Install or upgrade in graphical mode by pressing the enter key

Test the CD Media

You should test the CDs before you use them for the first time. Use the tab key to highlight the OK button, then press the space bar to initiate testing.

Skip testing the media by using the tab key to highlight the Skip button, then press the space bar.

Welcome to Fedora Core

On the Welcome to Fedora Core screen, read the text on the left, then click the Next button.

Language Selection

On the Language Selection screen, select the language you want to use during the installation process, then click the Next button.

Keyboard Configuration

On the Keyboard Configuration screen, select the appropriate keyboard for the system, then click the Next button.

Upgrade Examine

The installer searches for an existing installation of Fedora Core. If the installer detects that a version of Fedora Core is already installed on the computer, it presents the Upgrade Examine screen, which gives you the option to Install Fedora Core or Upgrade an existing installation. These directions follow the Install Fedora Core path. Select Install Fedora Core, then click the Next button.

If Fedora Core is not already installed on the computer, then the installer omits the Upgrade Examine step.

Installation Type

On the Installation Type screen, select Server, then click the Next button.

Disk Partitioning Setup

On the Disk Partitioning Setup screen, select Automatically partition, then click the Next button.

Automatic Partitioning

Partitioning sets up the hard drive so it can hold the Fedora Core 4 installation. You may already have another operating system installed on the computer (such as Windows XP) that you want to preserve. On the Automatic Partitioning screen, carefully select the choice that is most appropriate.

For a dedicated web server, you will normally want to select the second option, Remove all partitions on this system, and these directions assume that you make this choice. This choice wipes out everything previously installed on the computer.

However, on a dual boot machine that can boot Windows and a previous installation of GNU/Linux, you want to check Remove all Linux partitions on this system. This choice wipes out the previous GNU/Linux installation but preserves the Windows installation.

If Windows is installed and GNU/Linux is not already installed, you must have free disk space reserved for the GNU/Linux installation. In this case, select Keep all partitions and use existing free space.

Click the Next button.

Disk Setup

On the Disk Setup screen, check that Automatic Partitioning has set up your drives the way you desire. Click on the Back button to return to the previous step if necessary.

When finished with this step, click the Next button.

Boot Loader Configuration

On the Boot Loader Configuration screen, accept the default options. You want the GRUB boot loader installed; this will allow you to boot into other operating systems if you have a dual boot machine. Click the Next button.

Network Configuration

On the Network Configuration screen, you can set up your computer to run initially using DHCP, then later modify the network settings to assign a static IP address and host name. These directions assume you set the hostname automatically via DHCP, the default setting. Click the Next button.

Firewall Configuration

On the Firewall Configuration screen, select Enable firewall. Check the following options:

• Remote Login (SSH)
• Web Server (HTTP, HTTPS)
• File Transfer (FTP)

These directions ignore the Mail Server (SMTP) option.

For Enable SELinux, select Warn from the popup menu.

Click the Next button.

Time Zone Selection

On the Time Zone Selection screen, using the scrolling list to select your time zone. Click the Next button.

Set Root Password

On the Set Root Password screen, enter a high-quality root password and confirm it. A high-quality root password is about 15 characters long with a relatively random assortment of upper case and lower case letters, numerals, and punctuation characters. Click the Next button.

Package Group Selection

On the Package Group Selection screen, select the software you want to install on the computer. My recommendations are given in the table below. These recommendations are based on the premise that you are setting up a Linux server with a MySQL database, the Apache httpd web server, and that you’re going to create dynamic web pages using Perl and/or PHP. You will make different choices if you plan to use your computer for different purposes.

After the installation is complete, you can use the Add Programs utility to install additional packages from the CDs. And these instructions will show you how to use the yum utility to update existing packages and to install new packages.

Package Group	Selected	Notes
X Window System	Yes	Accept the default options.
GNOME Desktop Environment	Yes	Accept the default options.
KDE (K Desktop Environment)	No
Editors	No	The GNOME gedit text editor, which performs syntax highlighting, will probably suit your needs.
Engineering and Scientific	Yes	Click on the Details link and select gnuplot.
Graphical Internet	Yes	Click on the Details and select firefox as the only optional package to be installed.
Text-based Internet	No
Office/Productivity	No
Sound and Video	No
Authoring and Publishing	No
Graphics	No	You will install the graphics software later.
Games and Entertainment	No
Server Configuration Tools	Yes	Click on the Details link, and select just the following four optional packages: system-config-httpd system-config-securitylevel system-config-services xorg-x11-xauth
Web Server	Yes	Fedora Core 4 comes with Apache httpd version 2.0.54 and PHP version 5.0.4. Click on the Details link and select the optional packages you desire. I recommend: crypto-utils distcache httpd-manual mod-perl mod_ssl php php-mysql
Mail Server	No
Windows File Server	No
DNS Name Server	No
FTP Server	Yes	Accept the default option.
PostgresQL Database	No
MySQL Database	Yes	Click on the Details link and select the optional packages you desire. I recommend: mysql-devel mysql-server perl-DBD-MySQL php-mysql
News Server	No
Network Servers	No
Legacy Network Server	No
Development Tools	Yes	Accept the default options.
X Software Development	No
GNOME Software Development	No
KDE Software Development	No
Legacy Software Development	No
Java Development	No
Eclipse	No
Language Support	No
Administration Tools	Yes	Accept the default options.
System Tools	No
Printing Support	No
Everything	No
Minimal	No

Click the Next button.

About to Install

On the About to Install screen, read the text carefully, then click the Next button.

Required Install Media

Make sure you have all four Fedora Core 4 CDs to hand. If you followed these directions, you’ll require CDs #1, #2, #3, and #4. In the Required Install Media window, click the Continue button.

Installing Packages

The Installing Packages screen will provide status messages during the installation and prompt you to exchange CDs when required.

When the installation is complete, remove the last CD from the drive, connect the computer to your network, and click the Reboot button.

Reboot

When you reboot, if you also have Windows or another operating system installed on your machine, the GRUB booter will give you a few seconds to enter a menu and choose which operating system to boot. If you don’t respond, GRUB will boot Fedora Core 4 automatically.

Welcome

After reboot, Fedora Core will provide a Welcome screen that begins the steps for completing the setup of the system. Click the Next button.

License Agreement

On the License Agreement screen, read the license agreement, select Yes, I agree to the License Agreement, and click the Next button.

Date and Time

On the Date and Time screen, set the correct date and time, then click the Next button.

Display

On the Display screen, set the correct monitor type, resolution, and color depth for your display.

For my Toshiba Satellite Pro laptop, I clicked the Configure button, chose Generic LCD Display, selected LCD Panel 1400 x 1050, and clicked the OK button.

When finished, click the Next button.

System User

On the System User screen, set up an account for a normal system user. (You should use the root account only for system administration tasks.) When finished, click the Next button.

Sound Card

If the installer detected a compatible sound card in your computer, it presents the Sound Card screen. Test your sound card if you want to. When finished, click the Next button.

Additional CDs

On the Additional CDs screen, install software from additional CDs if you have any. These instructions assume that you have only the four Fedora Core 4 installation CDs and that there is nothing else to install. Click the Next button.

Finish Setup

On the Finish Setup screen, click the Next button.

Log In

Fedora Core will finish booting and present the login screen. Log in as the root user.

Update Fedora Core 4

Fedora Core 4 was released in June, 2005, and there have been many updates since. Follow these instructions to use the yum utility to apply the updates and install additional software.

Open Terminal

To open the Terminal application, which provides a command line prompt, click the Applications menu, select System Tools, then select Terminal. The default prompt for the root user will look something like this:

[root@localhost ~]#

For all commands given below, the prompt will be shown as:

#

Do not enter the prompt when you enter commands.

Update Fedora Core 4 with yum

In the Terminal window, use yum to update Fedora Core 4 by entering the command:

# yum update

This begins the update process, which takes a long time. The yum utility determines which packages need to be updated and provides the following prompt:

Is this ok [y/N]:

Enter y to initiate downloading the packages. The downloads take a few minutes to a few hours, depending on the speed of your Internet connection and on which mirror yum chooses. Once the packages have been downloaded, yum installs them, a process that can minutes to hours depending on the capabilities of your computer.

Once the update is complete, reboot the computer. From the Desktop menu, select Log Out. In the dialog box that appears, select Restart the computer and click the OK button.

Kernel Cleanup

After the update, there will be at least two and possibly more kernels installed on your server. You only need one of these. (On reboot, the GRUB boot loader allows you to specify which kernel your server should run.)

To identify the kernels installed on your server, open a Terminal window by right-clicking on the desktop and selecting Open Terminal from the menu. In the Terminal window, enter the following command:

# yum list installed "kernel*"

The output may look something like this:

# yum list installed "kernel*"
Installed Packages
kernel.i686                              2.6.14-1.1644_FC4       installed
kernel.i686                              2.6.11-1.1369_FC4       installed
kernel-devel.i686                        2.6.11-1.1369_FC4       installed
kernel-devel.i686                        2.6.14-1.1644_FC4       installed

If the list includes kernel-smp.i686 packages, these are Symmetric MultiProcessing kernels, which are designed for multi-processor computers.

You can remove the outdated kernel.i686 and kernel-devel.i686 packages with the following commands:

# yum remove kernel-2.6.11-1.1369_FC4.i686
# yum remove kernel-devel-2.6.11-1.1369_FC4.i686

When you restart your server, GRUB finds only the single remaining kernel.

Start and Test the Web Server

Fedora Core 4 installs the Apache httpd web server but doesn’t start it. Click on the Desktop menu, select System Settings, select Server Settings, and select Services. This opens the Service Configuration utility.

On the left hand side, scroll down to httpd and click the check box to its left. Then click the Start button in the row of buttons near the top of the window. A dialog box will appear named Information with the message httpd start successful. Click the OK button.

In the Service Configuration window, click on the File menu and select Save Changes. Then click on the File menu and select Quit. This configures the Apache httpd service to start automatically upon reboot.

Open the FireFox application by clicking on the Applications menu, selecting Internet, then selecting FireFox Web Browser. Enter the URL http://localhost/. The Fedora Core Test Page will appear. This confirms that the Apache httpd web server is functioning normally. To view the documentation for the web server, use the URL http://localhost/manual/.

If the httpd service doesn’t appear in the Service Configuration window, or if FireFox can’t open the default web page, then use yum to check that you have all the required packages installed. These are:

Functionality	RPMs	Version	Notes
Web Server	httpd.i386	2.0.54-10.2	Apache httpd web server.
	httpd-manual.i386
	apr.i386	0.9.6-3.5	Apache runtime library and utilities.
	apr-util.i386	0.9.6-2

Test the Apache httpd Server with PHP

Open the GNOME Text Editor by clicking on the Applications menu, selecting Accessories, and selecting Text Editor. Enter the following PHP code into the new file:

<?
    phpinfo();
?>

Save the file as /var/www/html/info.php. This file creates a dynamic, PHP-generated web page that reports the PHP configuration.

Open the FireFox web browser and navigate to http://localhost/info.php. If the web server and PHP are working correctly, a nicely formatted page should appear that describes the installation of PHP version 5.0.4 on the server.

Install Graphics, Numerics, and Software Development Packages

Required Packages

For a server that you’re going to use for bioinformatics data, you will want to install some or all of the following packages.

Functionality	RPMs	Version	Notes
zlib	zlib.i386	1.2.2.2-5.fc4	Compression support.
	zlib-devel.i386
libjpeg	libjpeg.i386	6b-34	JPEG image support.
	libjpeg-devel.i386
libtiff	libtiff.i386	3.6.1-10.fc3	TIFF image support.
	libtiff-devel.i386
libpng	libpng.i386	2:1.2.8-1.fc3	PNG image support.
	libpng-devel.i386
freetype	freetype.i386	2.1.9-1	Freetype font support.
	freetype-devel.i386
gd	gd.i386	gd.i386	Image generation support.
	gd-devel.i386
	gd-progs.i386
netpbm	netpbm.i386	10.28-1.FC3.2	Image conversion support.
	netpbm-devel.i386
	netpbm-progs.i386
ghostscript	ghostscript.i386	7.07-33	PostScript and PDF language interpreter.
	ghostscript-fonts.noarch	5.50-13
gnuplot	gnuplot.i386	4.0.0-4	Portable command-line driven interactive data and function plotting utility.
gcc	cpp.i386	3.4.4-2.fc3	GNU compiler collection.
	gcc.i386
	gcc-c++.i386
	gcc-g77
	gcc-java.i386
	libgcc.i386
	libgcj.i386
	libgcj-devel.i386
	libstdc++.i386
	libstdc++-devel.i386
glibc	glibc.i686	2.3.5-0.fc3.1	GNU C standard library.
	glibc-common.i386
gsl	gsl.i386	1.5-1	GNU Scientific Library, a numerical library for C and C++.
	gsl-devel.i386
make	make.i386	1:3.80-5	GNU make system.
automake	automake.noarch	1.9.2-3	GNU automake system for automated generation of Makefiles.
autoconf	autoconf.noarch	2.59-5	GNU automated configuration system.
libtool	libtool.i386	1.5.6-4.FC3.2	GNU generic library support script.
	libtool-libs.i386
bash	bash.i386	3.0-18	GNU bash shell or command language interpreter.
sed	sed.i386	4.1.2-4	GNU streams editor for text filtering.
awk	gawk.i386	3.1.3-9	GNU awk scripting language.
java	java-1.4.2-gcj-compat-devel.noarch	1.4.2.0-11jpp	Java programming support.
	ecj.i386	2.1.3-5
	java-1.4.2-gcj-compat.noarch	1.4.2.0-11jpp
	katana.noarch	2.0.0-1
httpd	httpd-devel.i386	2.0.53-3.3	Required to compile and install PHP 4.4.1.
	apr-devel.i386	0.9.4-17
	apr-util-devel.i386	0.9.4-17
	pcre-devel.i386	4.5-3.1.1.fc3

Install Required Packages with yum

Use the yum utility to identify which of these packages is missing, and install the missing packages. To determine if a set of packages is installed, use a command like the following:

# yum list installed "zlib*"
Installed Packages
zlib.i386                                1.2.2.2-5.fc4          installed
zlib-devel.i386                          1.2.2.2-5.fc4          installed

In this case, the required zlib packages are already installed. However, for libjpeg, the result is:

# yum list installed "libjpeg*"
Installed Packages
libjpeg.i386                             6b-34                  installed

For this example, libjpeg.i386 is installed, but libjpeg-devel.i386 is not. Install libjpeg-devel.i386 with the following command:

# yum install libjpeg-devel.i386

You can use yum to install several programs simultaneously. For example:

# yum install gd.i386 gd-devel.i386 gd-progs.i386

I found that I had to install the following packages, where indented package names indicate packages that were installed as prerequisites to the package being installed:

• libjpeg-devel.i386
• libtiff-devel.i386
• libpng-devel.i386
• freetype-devel.i386
• gd.i386
• gd-devel.i386
• gd-progs.i386
• netpbm.i386
• netpbm-devel.i386
• netpbm-progs.i386
• gnuplot.i386
• gsl.i386
• gsl-devel.i386
• java-1.4.2-gcj-compat-devel.noarch
  • ecj.i386
  • java-1.4.2-gcj-compat.noarch
  • katana.noarch
• httpd-devel.i386
  • apr-devel.i386
  • apr-util-devel.i386
  • pcre-devel.i386

Install PHP 4

There are two versions of PHP, PHP version 4 and PHP version 5. At the time of writing, the latest release of PHP version 4 is PHP 4.4.1.

Download PHP Source Code

Open the FireFox web browser and navigate to the PHP project’s downloads page at http://www.php.net/downloads.php. Under PHP 4.4.1 Complete Source Code, click on the link for PHP 4.4.1 (tar.gz). On the next page, choose a mirror site from which to download the source code. In the dialog box that appears, tell FireFox to save the file to disk.

Compile and Install PHP

Open a Terminal window by right-clicking on the Desktop and selecting Open Terminal. In the Terminal window, execute the following commands, which move the archive to root’s home directory /root, extract the source code from the archive, and configure the build instructions. To simplify the entering of the configuration options, I have placed each option on its own line. You may combine all the options to a single line by omitting the "\" characters.

# cd /root
# mv Desktop/php-4.4.1.tar.gz /root/
# tar -zxf php-4.4.1.tar.gz
# cd php-4.4.1
# ./configure                  \
  --with-apxs2                 \
  --with-gd                    \
  --with-pear                  \
  --with-jpeg-dir=/usr/lib     \
  --with-zlib-dir=/usr/lib     \
  --with-png-dir=/usr/lib      \
  --with-freetype-dir=/usr/lib \
  --with-mysql=/usr            \
  --enable-sockets             \
  --enable-mbstring

If there is an error at the configure step, it is because a Fedora Core 4 package is missing (e.g., freetype-devel.i386). The error message from the configure script will report what is missing. Refer to Install Server Support Software to identify and install the missing Fedora Core 4 package, then run the ./configure command again.

Note that the directory associated with the --with-mysql option is just /usr.

Compile and install PHP 4.4.1 with the following commands:

# make
# make install

Configure PHP

Following the installation directions provided by the file /root/php-4.4.1/INSTALL, copy the file /root/php-4.4.1/php.ini-recommended to /usr/local/lib/php.ini with the following command:

# cp /root/php-4.4.1/php.ini-recommended /usr/local/lib/php.ini

Using your favorite editor, establish the following settings in the file /usr/local/lib/php.ini, where the lines you must change are show in red:

Line No.	Setting
89	short_open_tag = On
246	memory_limit = 200M
285	error_reporting = E_ALL
292	display_errors = Off
302	log_errors = On
380	register_globals = Off
388	post_max_size = 200M
397	magic_quotes_gpc = Off
400	magic_quotes_runtime = Off
497	file_uploads = On
504	upload_max_filesize = 200M

Reconfigure the Apache httpd Server

Now reconfigure the Apache httpd server to use PHP. Using your favorite editor program, open the file /etc/httpd/conf/httpd.conf, which is the configuration file for the Apache httpd server. Below line 798, which is:

AddType application/x-gzip .gz .tgz

add the following lines:

#
# PHP support
#
AddType application/x-httpd-php .php .phtml

Now move to line 376, which looks like:

DirectoryIndex index.html index.html.var

and change the line by adding index.phtml and index.php:

DirectoryIndex index.html index.html.var index.phtml index.php

Restart the httpd server so it will recognize the new configuration and use PHP. Click on the Applications menu, select System Settings, select Server Settings, and select Services. This opens the Service Configuration utility.

On the left hand side, scroll down to httpd and select it. Its check box should be checked. Click the Restart button in the row of buttons near the top of the window. A dialog box appears named Information with the message httpd restart successful. Click the OK button, then close the Service Configuration window.

Test the Apache httpd Server with PHP

Using your favorite editor, create a new file with the following contents:

<?
    phpinfo();
?>

Save the file as /var/www/html/info.php. This creates a dynamic, PHP-generated web page that reports the PHP configuration.

Open the FireFox web browser and navigate to http://localhost/info.php. If the web server and PHP are working correctly, a nicely formatted page should appear that describes the PHP installation on the server.

Install phpMyAdmin

The easiest way to administer the MySQL database is to use phpMyAdmin, a MySQL management tool written using PHP. At the time of writing, the latest release of phpMyAdmin is 2.6.4-pl3.

Download phpMyAdmin

Open the FireFox web browser and navigate to http://www.phpmyadmin.net/home_page/index.php. On the left side of the page, under QUICK DOWNLOADS Latest stable version: phpMyAdmin 2.6.4-pl3, click on the link labeled gzip. On the next page, select a mirror site from which to download the software. When the download begins, tell FireFox to save the file to disk.

Install phpMyAdmin

The installation directions included with the source code say to unpack the archive directly into the document root directory of the web server. This directory is /var/www/html. Open a terminal window by right-clicking on the desktop and selecting Open Terminal from the window. Execute the following commands, which move the phpMyAdmin source code archive to /var/www/html, extract the archive, create a symbolic link, and change the owner of the phpMyAdmin files.

# mv /root/Desktop/phpMyAdmin-2.6.4-pl3.tar.gz /var/www/html/
# cd /var/www/html
# tar -zxf phpMyAdmin-2.6.4-pl3.tar.gz
# rm -f phpMyAdmin-2.6.4-pl3.tar.gz
# ln -s phpMyAdmin-2.6.4-pl3 phpMyAdmin
# chown -R root:root phpMyAdmin-2.6.4-pl3

Open the FireFox web browser and navigate to http://localhost/phpMyAdmin/. If the installation is successful, you see a Welcome to phpMyAdmin page.

Configure phpMyAdmin

The configuration file for phpMyAdmin is /var/www/html/phpMyAdmin/config.inc.php. Use your favorite editor to open and modify this file. There are only two changes to be made:

On line 62, change 'tcp' to 'socket':

$cfg['Servers'][$i]['connect_type']  = 'socket';         // How to connect...

On line 73, change 'config' to 'http':

$cfg['Servers'][$i]['auth_type']     = 'http';           // Authentication...

Reconfigure MySQL Using phpMyAdmin

As an example, you will use phpMyAdmin to create a database named bioinfodb, and you will create a MySQL user, bioinfo, who controls that database.

MySQL 4.1.15 is installed with four authorized users who have no passwords:

• root@localhost
• root@localhost.localdomain
• any@localhost
• any@localhost.localdomain

You will use phpMyAdmin to set up a root password for user root@% and to set up a second user account for user bioinfo@%. This allows user root and user bioinfo to log in from any machine. The root user will have global privileges. The bioinfo user will have specific privileges on the bioinfodb database.

Create Database

Open the FireFox web browser and navigate to http://localhost/phpMyAdmin/, and log in as user root with no password.

Click on the Databases link. At the bottom of the page, under Create new database, enter bioinfodb in the text entry field. For the collation (the character sorting order), select utf8_unicode_ci in the utf8 set. Click the Create button. This completes creation of the bioinfodb database.

Configure Users

At the top of the page, click on the Server: localhost link. In the page that appears, click on the Privileges link. In the User overview page that appears, there may be a warning:

Warning: Your privilege table structure seem to be older than this MySQL version! Please run the script mysql_fix_privilege_tables that should be included in your MySQL server distribution to solve this problem!

If this warning appears, minimize the phpMyAdmin window, and open a Terminal window by right-clicking on the desktop and selecting Open Terminal from the menu. Enter the mysql_fix_privilege_tables command:

# mysql_fix_privilege_tables
This script updates all the mysql privilege tables to be usable by
MySQL 4.0 and above.

This is needed if you want to use the new GRANT functions,
CREATE AGGREGATE FUNCTION, or the more secure passwords in 4.1

done
#

Return to the FireFox window. Click on the Privileges tab to refresh the window. The warning disappears.

The User Overview table lists four users. Check the checkboxes for user Any at host localhost, user Any at host localhost.localdomain, and user root at host localhost.localdomain. Under Remove selected users, select Delete the users and reload the privileges afterwards., then click the Go button.

The User overview table now shows only the single user, user root on host localhost. Click the icon at the furthest right in the row for this user to edit the user.

On the User 'root'@'localhost' page that appears, scroll down to Change password. Select Password and enter the password twice in the text entry fields, and click the Go button.

Click on the Privileges tab to log in again. Log in as user root with the password you just assigned. If necessary, click on the Privileges tab to return to the User overview page.

For user root on host localhost, click on the icon at the furthest right to edit the user.

On the User 'root'@'localhost' page that appears, scroll down to Change Login Information / Copy User. Click on the popup menu to the right of Host: and select Any host. The text entry field to the right changes from localhost to %. Click the Go button at the bottom of the page. This creates a new user, root on host %.

Click on the Privileges tab to view the two users. Click the checkbox for user root on host localhost. Under Remove selected users, select Delete the users and reload the privileges afterwords. and click the Go button. This completes the changes for the root user.

Click on the Privileges tab to view the User overview page. Click on the link Add a new User. In the Add a new User page that appears, for User name:, select Use text field: from the popup menu and enter bioinfo into the text entry field to the right. For Host:, select Any host from the popup menu. For Password:, select Use text field: from the popup menu, then enter the password twice in the text entry fields. Do not make any changes in the Global privileges part of the page. Click on the Go button.

phpMyAdmin confirms that it has created the new user and present the User 'bioinfo'@'%' page. Scroll down to Database-specific privileges. Click on the popup menu to the right of Add privileges on the following database and select bioinfodb. phpMyAdmin presents the User 'bioinfo'@'%'-Database bioinfodb page. Under Database-specific privileges, click on the link for Check All, then click the Go button.

This completes the configuration of user bioinfo.

Click on the Privileges tab to verify that there are now two users, root@% and bioinfo@%.

Test MySQL Configuration

Confirm that you can connect using either MySQL user. Open a Terminal window by right-clicking the desktop and selecting Open Terminal from the menu. Enter the following commands and confirm the responses from the MySQL client:

# mysql -u root -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 57 to server version 4.1.15-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> show databases;
+-----------+
| Database  |
+-----------+
| bioinfodb |
| mysql     |
| test      |
+-----------+
4 rows in set (0.00 sec)

mysql> exit
Bye
# mysql -u bioinfo -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 57 to server version 4.1.15-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> show databases;
+-----------+
| Database  |
+-----------+
| bioinfodb |
| test      |
+-----------+
4 rows in set (0.00 sec)

mysql> exit
Bye
#

Install Web Site Documents

Install web site document files in the /var/www/html directory.

Finish Network Configuration

If you configured your server to obtain its IP address using DHCP, you may want to assign it a static IP address so it can be found by other computers on your network. Use the following instructions to assign a static IP address.

Click on the Applications menu, select System Settings, and select Network. In the Network Configuration window that opens, click the Devices tab. Select the eth0 device and click the Edit button at the top of the window.

In the Ethernet Device window that opens, click on the Statically set IP addresses radio button. Set the static IP address. Contact your network administrator to learn what IP address, subnet mask, and default gateway address to use.

In the same Ethernet Device window, click on the Hardware Device tab. Check the box for Bind to MAC address and click the Probe button. Click on the OK button at the bottom of the window to close it.

In the Network Configuration window, click on the DNS tab. Set the Hostname (the name of your server). Set the Primary DNS. Set the DNS search path. Your network administrator can tell you the appropriate values for these fields.

In the same Network Configuration window, click the Hosts tab. Use the buttons at the top of the window to edit the hosts. This table can contain the names of hosts on your network and their corresponding IP addresses. Your network administrator can tell you the appropriate entries to make.

In the same Network Configuration window, click on the File menu and select Save. In the Information window that appears, click the OK button. Close the Network Configuration window.

Restart the server, then test it from another computer. You may need to use the IP address of your server to connect correctly. For example, if the IP address of your server is 192.168.0.2, open a web browser on another computer and navigate to http://192.168.0.2/. You should see the home page for your server.