Part II: The Bioinformatics Workstation
Chapter 3. Setting Up Your Workstation
3.2 Setting Up a Linux Workstation
3.2.1 Installing Linux
We can't possibly tell you everything you need to know to install and run Linux. That's beyond the scope of this book. There are many excellent books on the market that cover all possible angles of installing and running Linux, and you can find a good selection in this book's Bibliography. In this section, we simply offer some advice on the more important aspects of installation.
3.2.1.1 System requirements
Linux runs on a range of PC hardware combinations, but not all possible combinations.
There are certain minimum requirements. For optimum performance, your PC should have an 80486 processor or better. Most Linux users have systems that use Intel chips. If your system doesn't, you should be aware that while Linux does support a few non-Intel processors, there is less documentation to help you resolve potential problems on those systems.
For optimum performance your system should have at least 16 MB of RAM. If you're planning to run X, you should seriously consider installing more memory—perhaps 64 MB.
X runs well on 16 MB, but it runs more quickly and allows you to open more windows if additional memory is available.
If you plan to use your Linux system as a workstation, you should have at least 600 MB of free disk space. If you want to use it as a server, you should allow 1.6 GB of free space. You can never have too much disk space, so if you are setting up a new system, we recommend buying the largest hard drive possible. You'll never regret it.
In most cases the installation utility that comes with your distribution can determine your system configuration automatically, but if it fails to do so, you must be prepared to supply the needed information. Table 3-1 lists the configuration information you need to start your installation.
Table 3-1. Configuration Information Needed to Install Linux
Device Information Needed
Hard drive(s)
The number, size, and type of each hard drive
●
Which hard drive is first, second, and so on
●
Which adapter type (IDE or SCSI) is used by each drive
●
For each IDE drive, if the BIOS is set in LBS mode
●
RAM ● The amount of installed RAM
CD-ROM drive(s)
Which adapter type (IDE, SCSI, other) is used by each drive
●
For each drive using a non-IDE, non-SCSI adapter, the make and model of the drive
●
SCSI adapter (if any) ● The make and model of the card Network adapter (if any) ● The make and model of the card
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Mouse
The type (serial, PS/2, or bus)
●
The protocol (Microsoft, Logitech, MouseMan, etc.)
●
The number of buttons
●
For a serial mouse, the serial port to which it's connected
●
Video adapter
The make and model of the card
●
The amount of video RAM
●
To obtain information, you may need to examine your system's BIOS settings or open the case and look at the installed hardware. Consult your system documentation or your system administrator to learn how to do so.
Here are three of the more popular Linux distributions:
Red Hat (http://www.redhat.com/support/hardware/)
All have well-organized web sites with information about the hardware their distributions support. Once you've collected the information in Table 3-1, take a few minutes to check the appropriate web site to see if your particular PC hardware configuration is supported.
3.2.1.2 Partitioning your disk
Linux runs most efficiently on a partitioned hard drive. Partitioning is the process of dividing your disk up into several independent sections. Each partition on a hard drive is a separate filesystem. Files in one filesystem are to some extent protected from what goes on in other filesystems. If you download a bunch of huge image files, you can fill up only the partition in which your home directories live; you can't make the machine unusable by filling up all the available space for essential system functions. And if one partition gets corrupted, you can sometimes fix the problem without reformatting the entire drive and losing data stored in the other partitions.
When you start a Red Hat Linux installation, you need the Linux boot disk in your floppy drive and the Linux CD-ROM in your CD drive. When you turn the computer on, you almost immediately encounter an installation screen that offers several installation mode options. At the bottom of the screen, there is a boot: prompt. Generally, you should just hit the Enter key; however, if you're using a new model of computer, especially a laptop, you may want to enter text, then press the Enter key for a text-mode installation, in case your video card isn't supported by the current Linux release.
Click through the next few screens, selecting the appropriate language and keyboard. You'll come to a point at which you're offered the option of selecting a GNOME workstation, a KDE workstation, a server, or a custom installation. At this point, you can just choose one of the single user workstation options, and you're essentially done. However, we suggest doing a custom installation to allow you greater control over what is installed on your computer and where it's installed.
If you have a single machine that's not going to be interacting with other machines on the network, you can probably get away with putting the entire Linux installation into one big filesystem, if that's what you want. But if you're setting up a machine that will, for instance, share software in its /usr/local directory with all the other machines in your lab, you'll want
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to do some creative partitioning.
On any given hard disk, you can have four partitions. Partitions can be of two types: primary and extended. Within an extended partition, you can have as many subpartitions as you like.
Red Hat and other commercial Linux distributions have simple graphical interfaces that allow you to format your hard disk. More advanced users can use the fdisk program to achieve precise partitioning. Refer to one of the "Learning Linux" books we recommend in the Bibliography for an in-depth discussion of partitioning and how to use the fdisk program.
3.2.1.3 Selecting major package groupings
After you've set up partitions on your disk, chosen mount points for your partitions, and completed a few other configuration steps, you need to pick the packages to install.
First, go through the Package Group Selection list. You'll definitely need printer support; the X Window System; either the GNOME or KDE desktop (we like KDE); mail, web, and news tools, graphics manipulation tools; multimedia support; utilities; and networked workstation support. If you'll be installing software (and you will), you need a number of items in the development package group (C, FORTRAN, and other compilers come in handy, as do some development libraries). You may also want to install the Emacs text editor and the
authoring/publishing tools. Depending on where you use your system from, you may need dial-up workstation support.
The rest of the package groups add server functionality to your machine. If you want your machine to function as a web server, add the web server package group. If you want to make some of the directories on your machine available for NFS mounting, choose the NFS server group. If you plan to create your own databases, you may want to set up your machine as a PostgreSQL server. Generally, if you have no idea what it is or how you'd use it, you probably don't need to install it at this point.
If you're concerned about running out of space on your machine, you can now sift through the contents of each package grouping and get rid of software you won't be using. For example, the "Mail, Web and News" package grouping contains many different types of software for reading email and newsgroups. Don't install it all, just pick your favorite package, and get rid of the rest. (In case you're wondering what to choose, here's a hint: it's very easy to configure the Netscape browser to do all the mail and news reading you'll need.) If you're installing a Red Hat system, check under "Applications/Editors" and make sure you have the vim editor selected; in "Applications/Engineering," select gnuplot; and in
"Applications/Publishing," select enscript. Don't worry if you don't install something at the beginning and find you need to install it later, it's pretty easy to do.
3.2.1.4 Other useful packages to add
Once you've done a basic Linux installation on your machine, you can add new packages easily using the kpackage command (if you're using the KDE desktop environment) or gnorpm (if you are using GNOME).
In order to compile some of the software we'll be discussing in the next few chapters, and to expand the functionality of your Linux workstation, you may want to install some of the following tools. The first set of tools are from the Red Hat Linux Power Tools CD:
R
A powerful system for statistical computation and graphics. It's based on S and consists of a high-level language and a runtime environment.
OpenGL /Mesa
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A development kit for creating graphical user interfaces that enhances performance of some molecular visualization software.
LessTif
A widget set for application development. You might not use it directly, but it's used when you compile some of the software discussed later in this book. Install at least the main package and the client package.
Xbase
Another widget set.
MySQL
A database server for smaller data sets. It's useful if you're just starting to build your own databases.
octave
A MatLab-like high-level language for numerical computations.
xv
A multipurpose image-editing and conversion tool.
xemacs
A powerful X Windows-based editor with special extensions for editing source code.
plugger
A generic Netscape plug-in that supports many formats.
You can download from the Web and install the following tools:
JDK /JRE (http://java.sun.com)
A Java Development Kit and Java Runtime Environment are needed if you want to use Java-based tools such as the Jalview sequence editor we discuss in Chapter 4. They are freely available for Linux from IBM, Sun, and Blackdown (http://blackdown.org).
Blackdown also offers a Java plug-in for Netscape, which is required to run some of the applications we discuss.
NCBI Toolkit ( ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/README.htm)
A software library for developers of biology applications. It's required in order to compile some software originating at NCBI.
StarOffice (http://www.staroffice.com)
A comprehensive office productivity package freely available from Sun Microsystems.
It replaces most or all functionality of Microsoft Office and other familiar office-productivity packages.
Delivered for Maurice ling Swap Option Available: 7/15/2002
Last updated on 10/30/2001 Developing Bioinformatics Computer Skills, © 2002 O'Reilly
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Index terms contained in this section
extended/primary partitions installing Linux and installing
Linux
Intel chips, installing Linux Internet
downloading and installing JDK/JRE Iobion Systems
Java
Development Kit (JDK) Runtime Environment (JRE)
JDK (Java Development Kit), downloading and installing JRE (Java Runtime Environment)
NCBI (National Center for Biotechnology Information) Toolkit (software library)
Package Group Selection list, installing Linux partitioning, dividing hard drives
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SCSI adapters, installing Linux servers
installing Linux and StarOffice office package SuSE (Linux distributor) VA Linux
video adapters. installing Linux workstations
Linux, setting up X Window System Xbase widget set xemacs editor
xv image editing/conversion tool
© 2002, O'Reilly & Associates, Inc.
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