Documentation

A Dummy's Guide To Starting With BioSLAX

BioSLAX

BioSLAX is a bioinformatics variant of SLAX which is a live DVD/USB thumbdrive. A Live DVD/ USB thumbdrive is a complete operating system (OS) running off the DVD/USB thumbdrive, making use of your computer.s memory to load itself. The BioSLAX CD/USB thumbdrive runs the Linux Slackware OS. The system can be totally isolated from and independent of whatever OS already installed in your hard drive (eg. Windows XP, Windows Vista, etc). However, the OS will be able to access the files on those hard drives.

In this way, you need not have to reformat your hard drive to install BioSLAX and all your existing data stays intact. From the BioSLAX operating system booted up on your PC, you can access all key bioinformatics software.

BioSLAX will boot on Intel MACs, but it has not been fully tested.

Getting a copy of BioSLAX

There are several ways of booting BioSLAX, but all of them will involve the initial step of obtaining the BioSLAX iso image and burning it into a bootable DVD. You can download the latest BioSLAX iso from the downloads section.

Creating a Bootable DVD

Once you get the iso copy of the BioSLAX, you should make a backup copy of it.

Using any software that allows burning of DVDs from iso files (eg, Nero, EZ media creator, or Magic ISO) you can burn the iso file you have downloaded into a bootable DVD. This is NOT the same as copying the iso file into the DVD. Burning the image means transferring the entire image of the iso file including the file system and all its constituent files into the DVD, instead of copying the iso file into the DVD's file system.

Creating a Bootable USB thumbdrive

Alternatively, you may create a bootable USB thumbdrive from the ISO image.

First, format your USB thumbdrive (must be of capacity 2GB and above) as a FAT or FAT32 filesystem using your Windows format utility.

Then, using any software that can extract files from an ISO (eg. Magic ISO, WinISO or WinRAR), extract the contents of the ISO into your USB thumbdrive. You will find 2 directories in your thumbdrive after this, boot and bioslax.

Using a DOS command prompt (Windows Start button, click Run, then type in .cmd. without the quotes into the textbox and hit enter), CD to the boot directory. Now run the file called bootinst.bat. It will show you the following text :

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=                                     Welcome to Slax boot installer =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= This installer will setup disk %DISK%: to boot only Slax. Warning! Master Boot Record (MBR) of the device %DISK%: will be overwritten. If %DISK%: is a partition on the same disk drive like your Windows installation, then your Windows will not boot anymore. Be careful! Press any key to continue, or kill this window [x] to abort...

Where %DISK% is the drive letter of your USB thumbdrive. Hit any key make your USB thumbdrive bootable.

IMPORTANT! Using a bootable USB thumbdrive will only work if the machine you are booting from supports booting from external USB devices. If it does not, the machine will not recognize the thumbdrive as bootable and will not boot BioSLAX from it.

Starting BioSLAX by booting from the Live DVD/USB thumbdrive

Method 1: Booting directly from the DVD/USB thumbdrive

If booting from the DVD, switch on the PC, and quickly press the DVD Drive hatch to get it to open. You only have a few seconds to do this. Pop the DVD into your CD drive, and REBOOT the computer into BioSLAX.

If booting from the USB thumbdrive, plug your USB thumbdrive into any available USB slot and reboot the computer.

Ensure your BIOS options are set to boot from the DVD drive or USB thumbdrive before booting from the hard drive. This is called the Boot Device Priority of the BIOS.

There are two ways of doing this:

• Selecting DVDROM or USB device as the boot device when starting the computer.


When you switch on the computer, you will see a line of instructions asking you to press F12 (or some other key depending on the PC) for you to select Boot Menu. Press it, then select to boot from the DVD Drive or the USB device.

Typically, the options may look like as follows:

Boot Menu

Floppy Disk
USB Device
Hard Disk
DVD Rom
Network

When you see this screen, use the arrow keys to move up and select the DVDROM option (if you are booting from DVD) or the USB DEVICE option (if you are booting from a USB thumbdrive), and press ENTER. The boot sequence will then read from the DVD Rom or USB thumbdrive, where BioSLAX is located.

If this doesn't work, try option b. If it works, skip the next step.


• Configuring your Boot Device Priority of the BIOS of your PC.
  
  When you boot up your computer, press F2 (or ESC, or DELETE, etc, depending on your PC) to enter into the BIOS Configuration mode. Select the BOOT tab, and the BOOT device priority list. Select DVDROM or USB Device to be the first boot device by using the arrow key or PgUp depending on your PC. Save and Exit (typically pressing F10).
  
  When this is configured properly, the PC knows to boot from the DVDROM or USB DEVICE first (instead of the usual HardDisk). BioSLAX will then start to load as the operating system.
  
  
  Figure 1. BioSLAX booting up
  
  When it does boot up from BioSLAX, you will see the BioSLAX splash screen as in the first diagram in Figure 1.
  
  BioSLAX has several booting modes to cater for different experiences and hardware. For most of the new PCs and laptops, the first option should be fine. If you are having trouble with your display, choose the 2nd option which is the Safe option. If any of your hardware fails to work, try to boot with the other (No ACPI or No PCMCIA) options.
  
  

Method 2: Booting from the BioSLAX files on a hard disk

Generally, a Pentium 4 machine with 512 Mbyte RAM is the minimum configuration that should just work. However, you might find that the overall experience of booting from the CD is too slow.

If so, you can make it boot faster, by having the system access the BioSLAX files from your hard disk. Reading data from the harddisk is generally faster than reading data from a LiveDVD in the DVDRom Drive.

There are 2 ways to boot from the harddisk,

• from files of BioSLAX copied into the hard disk
  
• from a single BioSLAX.iso file containing the BioSLAX image, copied into the hard disk.
  

Copying the contents of the DVD/USB thumbdrive onto your hard drive

Boot up as usual into your Microsoft Windows environment. Create a subdirectory on your Windows hard drive (eg; C:\SLAX) then copy the contents of the BioSLAX DVD or the USB thumbdrive to that directory. Just drag and drop the contents into the C:\SLAX directory in your file Explorer.

• IMPORTANT NOTE:
  
  In the Microsoft Windows (XP or Vista) environment, disk drives are typically labeled C: or D: for hard disks, A: for Floppy and E: for CDROM drives.
  
  Now, in the Linux OS, the different drives are not represented by letters (eg, A, C, D, etc). They are represented by devices. Again these are represented differently for IDE, SATA and SCSI hard disk drives. The following is a table showing the different representation of the different drives:
  
  

  Windows/DOS	Linux
  A	/dev/floppy
  C (first primary partition)	/dev/hda1 (for IDE drives) /dev/sda1 (for SCSI and SATA drives)
  D (first logical partition)	/dev/hda5 (for IDE drives) /dev/sda5 (for SCSI and SATA drives)

  
  
  Therefore C:\SLAX in the Microsoft Windows OS would be represented as /dev/sda1/slax to the Linux OS. Note that Linux is CASE SENSITIVE, so the case of the directory name matters.
  
  

Once you have copied the contents of the DVD onto your hard drive or have copied the BioSLAX ISO to your hard drive (eg C:\bslax.iso), you have to use the BioSLAX DVD or USB thumbdrive to boot up, and at the initial BioSLAX menu selection screen, press the TAB KEY while over any of the boot up selections of your choice.

In the following example, we will assume you are on option 2 (Safe option).

i. Press the TAB KEY while the selection bar is over option 2.
ii. You will see a line of text at the bottom.



Figure 2. Select your option and press the TAB KEY



Figure 3. Command text appears at the bottom after pressing the TAB KEY
iii. Press the space bar and then :

• If you want to boot from the BioSLAX files extracted to your hard drive (files in C:\SLAX), type from=/dev/sda1/SLAX
  
  
  
  Figure 4. Booting from BioSLAX files extracted to the hard drive


• B) If you want to boot from the ISO file (C:\bslax.iso), type from=/dev/sda1/bslax.iso
  
  
  
  Figure 5. Booting from a single BioSLAX ISO file on the hard drive

The system will start to boot up and will read the BioSLAX data from either the directory where the extracted BioSLAX files are or from the BioSLAX ISO file directly.

When the system boots up, you will see the device initialization screen and finally the X-Windows desktop.


Figure 6. BioSLAX device initialization screen and X-Windows desktop

TIP: Name your iso to something easier to type, like b.iso. All you have to type now is from=b.iso

How to connect to the Internet

Wired Connection

Plug your network cable to your PC and BioSLAX will auto detect it immediately and set up your network connections.

Wireless Connections BioSLAX has support for a variety of wireless cards and onboard wireless devices running the following chipsets:

• Intel 2100/2200/3945/4965
• Athereos
• TI ACX11x
• Broadcom

And many more. Most laptops today run on the Intel wireless 3945 or 4956 which is fully supported by BioSLAX.

Note:
WPA/WPA2 secured access points cannot be accessed using the wireless manager. This requires more command line configuration which will not be covered in this document.

Saving Changes

After doing your work on BioSLAX you may have made changes to the configuration. Every time you reboot your machine, ANY CHANGES YOU HAVE MADE WILL BE LOST. To prevent this, you need to Save Changes regularly.

For portable data (eg, documents, results files, etc) you can plug in your USB thumbdrive and save the data to the USB thumbdrive and then access it later even after rebooting, but how do you save system changes?

Firstly, determine what device your thumbdrive is identified as in linux. It may be identified as /dev/sdb1. It could also be sdc or sdd instead of sdb, depending on how many other sata/scsi devices you have on the computer. For this example, we will assume that it is /dev/sdb1.

Make a directory on the thumb drive called mychanges.

When booting up, again hit the TAB KEY when you are at the BioSLAX menu selection. The command text will appear at the bottom. Press the space key and enter the following:

changes=/dev/sdb1/mychanges



Figure 7. Setting up persistent changes
If you are booting from the extracted BioSLAX files or the BioSLAX iso, proceed as instructed in section 5, method 2, and type the changes= command after the from= command.

With this command, any changes or modifications you make will be saved AND restored from the mychanges directory on your thumbdrive.

For the more intuitive students, you will realize that you can create different directories on your thumbdrive to save different sessions of your BioSLAX runs. You may set up BioSLAX in different ways or run a sequence search using different programs and store the results individually, so that you may later do a comparison.

We trust that you have found this guide useful.