Transcript Setting up a Sendmail Mailserver BioInformatics

Using BioSlax and the BioSlax Server
Tin Wee Tan
National University of Singapore
Bioinformatic and Comparative Genome Analysis Course
HKU-Pasteur Research Centre - Hong Kong, China
August 17 - August 29, 2009
What is BioSlax?
• Slackware Linux on a CD + bioinformatics modules
included
• Released by Bioinformatics Centre (BIC), NUS
• Uses Unification File System (aufs) that allows readonly file system to have writable access by saving all
changes in memory
• Slax - created by Tomas Matejicek. Website is at:
http://www.slax.org/
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Why use BioSlax/Slax?
• Complete OS by itself running off a CD
• Uses computer’s memory to load itself
• Isolated from and independent of OS already
installed on hard disk (eg. Windows XP, Windows
Vista, etc)
• Need not format hard disk for installation. Existing
data stays intact
• Modular
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Modularity of BioSlax
• There are 2 parts to the BioSlax build
– Part 1: core system (Linux OS + basic tools)
– Part 2: modules
• Modules
– individual utilities user wants
– easily added or removed prior to CD creation
– easily upgraded when new version’s available
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Modules in BioSlax …
Bioinformatics Modules:
-BLAST
-PatScan
-Primer3
-PyMOL
-ClustalW
-T-Coffee
-Artemis ACT
-RasMOL
-ClustalX
-PHYLIP
-Artemis ART
-ReadSeq
-EMBOSS
-GeneSplicer
-jAlign
-TreeView
-Modeller
-GlimmerHMM
-Jalview
-PamL
-HMMER
-NjPlot
-Sequence
Manipulation
Suite v2
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Booting Up Bioslax
1. CD (without Open Office)
2. DVD (with Open Office)
3. USB drive (with Open Office)
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Configuring your Boot Device Priority
of the BIOS of your PC
• When you boot up your computer. Press F2 (or
F1/ESC/DELETE etc) to enter the BIOS Configuration
mode (Setup)
• Select the BOOT tab, and the BOOT device priority
list
• Select CD-Rom to be the first boot device by using
the arrow/F5/Pg Up key. If you are booting from USB
drive – Select “USB Key” to be the second boot
device
• Save and Exit
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – Bioslax Booting Up
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – Bioslax Booting Up
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Running Bioslax on Windows Using
VMware player
• Download and install VMware Player
– http://www.vmware.com/download/player/
• Download BioSlax Version Customized For
VMPlayer
– Unzip to C drive (e.g. C:\BS71VMCD)
– Run VMPlayer and open C:\ BS71VMCD \Other
Linux 2.6.x kernel.vmx
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Setting up your internet connection in
VMware version of Bioslax
• Change the network setting (on the top menu) from
“Bridged” to “NAT”
• Open Konsole
• Type “dhcpcd” and press “Enter”
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – VMWare Version
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
The X-Window Desktop
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
How to create a Slax module
• To convert tgz package to Slax module:
tgz2lzm <application.tgz> <application.lzm>
e.g. tgz2lzm blast.tgz blast.lzm
• To install an application to a separate directory:
dir2lzm <directory> module.lzm
e.g. dir2lzm /usr/local/blast blast.lzm
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
How to use a Slax module
• To create own LiveCD:
– save modules in /modules directory of the CD
• To activate a module, use:
activate </path/module.lzm>
e.g. activate /tmp/blast.lzm
• To deactivate a module, use:
deactivate </path/module.lzm>
e.g. deactivate /tmp/blast.lzm
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
How to save/restore settings
• To save and restore your settings, hit the ‘TAB’
key at the BioSLAX boot menu selection. Use:
changes=/mnt/sda1_removable/mychanges
where /mnt/sda1_removable is a mounted USB drive
and /.../mychanges is a directory created in the USB
drive to store settings
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Network setup
Open Konsole and type iwconfig to list all
possible wireless devices on the system
Wireless Asst  Select your wireless device (can be
referred to as wlanX, wifiX, athX, brX, ethX)
If you don't have a built in wireless device, plug in
your external wireless card before running Wireless
Asst.
Select DHCP and a pop up message will appear at
the bottom right if the card successfully obtains an
IP address. Run Mozilla, the web browser
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
• Insert your USB drive into the PC
• Make sure your USB drive is detected
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
• If you don’t see the db directory, open Konsole & type:
cd /mnt/sda1_removable/
wget ftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz
tar –zxf blast-db-demo.tar.gz
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
• To setup BLAST database, go to K-Menu ->
BioSLAX -> Desktop Apps -> BLAST DB Setup
• Fill in the location of the BLAST formatted
database files
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
• Start web BLAST & select the list of BLAST programs:
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
•Regular BLAST page
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
•BLAST result
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Recommended reading
1. http://www.slax.org/
2. http://www.bioslax.com/
3. http://www.slax.org/documentation.php
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Hands-On Practice
1. htdocs and cgi-bin folders
2. Modules
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Bioslax as server
1. Host BLAST database
2. Hosting web server
Copyright ⓒ 2009. National University of Singapore. All rights reserved.