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Using BioSlax and the BioSlax Server

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

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Using BioSlax and the BioSlax Server

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  1. 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

  2. What is BioSlax? • Slackware Linux on a CD + bioinformatics modules included • Released by Bioinformatics Centre (BIC), NUS • Uses Unification File System (aufs) that allows read-only file system to have writable access by saving all changes in memory • Slax - created by Tomas Matejicek. Website is at: http://www.slax.org/

  3. 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

  4. 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

  5. Modules in BioSlax … • Bioinformatics Modules:

  6. Booting Up Bioslax • CD (without Open Office) • DVD (with Open Office) • USB drive (with Open Office)

  7. 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

  8. Screenshot – Bioslax Booting Up

  9. Screenshot – Bioslax Booting Up

  10. 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

  11. 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”

  12. Screenshot – VMWare Version

  13. The X-Window Desktop

  14. 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

  15. 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

  16. 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

  17. 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

  18. Web BLAST demo • Insert your USB drive into the PC • Make sure your USB drive is detected

  19. Web BLAST demo • If you don’t see the db directory, open Konsole & type: • cd /mnt/sda1_removable/ • wgetftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz • tar –zxf blast-db-demo.tar.gz

  20. 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

  21. Web BLAST demo • Start web BLAST & select the list of BLAST programs:

  22. Web BLAST demo • Regular BLAST page

  23. Web BLAST demo • BLAST result

  24. Recommended reading • http://www.slax.org/ • http://www.bioslax.com/ • http://www.slax.org/documentation.php

  25. Hands-On Practice • htdocs and cgi-bin folders • Modules

  26. Bioslax as server • Host BLAST database • 2. Hosting web server

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