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apbioknoppix

Page history last edited by PBworks 5 years, 10 months ago

Apbioknoppix

 

Main Project Contributors: Chua Ruiwen, Luqman Hakim B Abdul Hadi and Goh Lu Feng

 

This page will document the step by step process on how we remaster Knoppix 5.0.1 to create Apbioknoppix 3.0.

 

NOTE: We did this re-mastering with 0 knowledge, therefore though research has been done, this is mainly trial and error.

 

System Requirements & Setup

 

This method is applicable to Knoppix versions later than 3.3. Earlier versions do not have the provision for the required 'Knoppix style' HD installation.

Any computer capable of running Knoppix can be used for remastering provided it has enough free space on the hard drive. Approximately 6 Gig of free space is required:

  • HD installed Knoppix......................................................min 2.3 Gig
  • assembled compressed file system......…........................700 Meg
  • final iso file system ready to burn to CD.........................700 Meg
  • combined RAM & swap space totalling 1 Gig...............500-700Meg
  • toHD Knoppix operating system.....................................700 Meg
  • Total................................................................….............6.1 Gig

 

For this example we are going to assume we are starting from a HD with some form of Windows on it which will be set up for dual boot as this is probably more typical than a Linux only system. Functionally, the only difference having the Windows system actually makes is to change the partition numbers.The recommended HD partition is as follows:

  • hda1...Windows O/S...............................………………..size as appropriate
  • hda5...Knoppix HD install...........................…………….min 2.3 Gig, 3-3.5 preferred
  • hda6...new remastered isos.....................………………..min 1.5 Gig
  • hda7...shared Windows/Linux data, VFAT format, all remaining space
  • hda8...Linux swap.............………………........................approx 500-700 Meg(swap size as needed to total 1Gig RAM + swap)

 

Install Knoppix

 

After partitioning, do a hardisk install of Knoppix.

 

$ sudo knoppix-installer

 

Choose the cd install (not Debain Install) and install the bootloader GRUB to the partition if you are already running Linux. Not too sure if you are running Windows.

 

Changing of Default Desktop.

 

Change default KDE to ICEWM at etc/sysconfig/Desktop and edit /etc/init.d/knoppix-autoconfig. Change value “DESKTOP=kde” to “DESKTOP=icewm” and comment out the 2nd line using "#" to bypass the getbootparam. This step changes the default desktop to icewm. (I bet you knew that!):

 

# Also read desired desktop, if any

#DESKTOP="$(getbootparam desktop 2>/dev/null)"

# Allow only supported windowmanagers

case "$DESKTOP" in gnome|enlightenment|kde|larswm|xfce|xfce4|windowmaker| wmaker|icewm|fluxbox|twm|nx|rdp|kiosk) ;; *) DESKTOP="icewm"; ;; esac

 

Ask xsession to function call icewm-session instead of icewm. This enables rox desktop and other icewm components to be started, instead of just icewm alone. Edit the file /etc/X11/Xsesssion.d/45xsession. This is the file that controls all the X configurations in Knoppix! Very impt fact!!!

 

Look for the function starticewm. This function will execute icewm. Change it to execute icewm-session.

 

starticewm(){

# Create automatic Desktop icons

mkdesktophdicons

playsound

GDK_USE_XFT=1 exec icewm-session

}

 

Removal of uneeded software.

 

Remove KDE language files:

$ sudo apt-get --purge remove kde-i18n*

 

Special mention goes to kdebluetooth (which is giving us a lot of problems)

$ sudo dpkg --purge kdebluetooth

$ sudo apt-get remove --purge kdebluetooth

 

Remove some KDE related stuffs:

 

$ sudo apt-get --purge remove kde-menu-knoppix kde-services-knoppix kdebase libkdegames1 kdead* kdegraphics kdemultimedia* kdeprint kdessh kdesktop kdepasswd kdenetwork* kdelock* kdegraphics* kdebase-data kdebase-kio*

 

Remove these too:

$ sudo apt-get remove --purge airsnort bluez-utils bluez-firmware bonnie++ britty btpin-knoppix buffer cddb debconf-il18n ethereal* etherwake ettercap-*

helix-player ijsgimpprint java-common java2-runtime-knoppix kamera kiconedit knode mozilla-firefox-locale-de* mozilla-thunderbird-locale-de nessus* nx* telnet* vcd* kmix kaffeine radio xawtv* digikam kview freemind kfax ktnef alevt units txt2regex nvtv ativout xtv dvbackup ktip ktimer ark klipper kpager kcharselect k3b khexedit ding kmenuedit* kpackage khelpcentre joe zile konsole kget xbattle ace-of-penguins xskat kalc kate kpdf kghostview kooka ksnapshot scribus kolourpaint kiconedit kfind filelight kappfinder kbackup

 

Remove fluxbox, kwin and wmaker:

$ sudo apt-get remove --purge kwin fluxbox wmaker larswm wmaker-data

wmakerconf-data

 

Remove unused shell:

$ sudo apt-get remove --purge kviewshell rootshell-knoppix ash-knoppix-26 sash dash

 

Do a purge of these:

$ sudo dpkg --purge xbattle

 

Installation of non-bio software

 

Install these:

$ sudo apt-get install amsn rox-filer gnotepad+ galculator xpaint gimageview gnome-iconedit

 

Installation of bio software:

 

Install these:

$ sudo apt-get install rasmol pymol clustalx bioperl blast2 t-coffee hmmer

 

Install Jalview by going to http://www.jalview.org/Web_Installers/install.htm and download the installer.

 

Install additional biosoftware deb packages from http://www.debian.org/devel/debian-med/microbio

 

After editing the apt sources.list based on instructions at http://debian.bioinformatics.unsw.edu.au/, use apt to install EMBOSS

  • Emboss (need to set repo in apt sources.list)

 

Settings

 

This sets default terminal emulator to rxvt

$ sudo ln –sf /usr/bin/rxvt /etc/alternatives/x-terminal-emulator

$ sudo ln –sf /usr/share/man/man1/rxvt.1.gz /etc/alternatives/x-terminal- emulator.1.gz

 

To change ‘Start’ menu programmes display, go to “/etc/X11/icewm/menu” and edit.

 

After installing initng, look for file ‘xsession.i’ and change to

#!/sbin/itype

  1. This is a i file, used by initng parsed by install_service

 

service system/xsession {

need = system/bootmisc system/initial;

script start = { /bin/bash /etc/init.d/xsession start};

}

 

 

initng causes some changes in default boot session. This is affected:

in “/etc/network/interfaces”

add auto lo eth0 # to first line

add iface eth0 inet dhcp # to last line

 

Change toolbar xterm to show black background by editing /etc/X11/icewm/toolbar. Ensure that the xterm entry includes the options as follows:

prog XTerm xterm rxvt -rv -C -fn 9x15 -sl 500

 

Change rox desktop to use double click instead of single click. Once rox has been started, juz right click on the deskop and go to rox-filer >options; filer window>window behaviour>single click navigation.

 

Change font size settings of FF for monospace and default font to 17.

 

Changes in the start menu tabs can be made by editing ~/.icewm/programs.

 

Mushroom wallpaper: http://wallpapers.jurko.net/pic/1439/

 

Use these theme:

http://themes.freshmeat.net/projects/elberg-icewm/

http://themes.freshmeat.net/projects/winclassic/

http://themes.freshmeat.net/projects/glamice2/

http://themes.freshmeat.net/projects/cubex/

http://themes.freshmeat.net/projects/xp__/

 

 

In ROX, we had this problem of always getting an error message for every icon clicked. This was rectified by going to ‘ROX Option’  ‘Filer windows’  ‘Windows behavious’ and uncheck ‘single click navigation’. Duh!

 

 

FAQ on how to make the icons available on ICEWM htpp://bbs.cvut.ca/~covex/icewm/iceicons/

 

Take out w3m

 

Kiv take out xedit nedit kate kwrite

 

To edit menus go here: /home/knoppix/.icewm/programs and /etc/X11/icewm/menu

 

Optimizations

 

Reduce workspace to 3 by editting the file “~/.icewm/preferences” and look for the section of workspaces. Change it to as follows:

 

# Names of the Workspaces

 

WorkspaceNames=" 1 "," 2 "," 3 "

 

Reduce spawned tty to reduce boot time .In this case, since initng is installed, we need to edit initng config files. Specifically, we edit the contents of /etc/initng/daemon/getty.i to:

 

#!/sbin/itype

# This is a i file, used by initng parsed by install_service

daemon daemon/getty/1 { need = system/bootmisc; provide = virtual/getty/${NAME}; term_timeout = 3; env DEV_PRE=tty; exec daemon = /sbin/getty 38400 ${DEV_PRE}${NAME}; respawn; last;

}

daemon daemon/getty/2 { need = system/bootmisc; provide = virtual/getty/${NAME}; term_timeout = 3; env DEV_PRE=tty; exec daemon = /sbin/getty 38400 ${DEV_PRE}${NAME}; respawn;

}

virtual daemon/getty { need = daemon/getty/2; use = system/mountfs system/netmount system/issue;

}

 

Reduce kernel swappiness (from http://www.linuxjournal.com/article/8308):

$ sudo cat /proc/sys/vm/swappiness #Continue if value<10.

$ sudo sysctl -w vm.swappiness=10

$ sudo cat /proc/sys/vm/swappiness #Value shld = 10 now.

 

Add to /etc/sysctl.conf and then restart:

vm.swappiness=10

 

Increasing Ooo perfornance(from http://openoffice.blogs.com/openoffice/2006/04/optimizing_open.html):

 

Do not run wif JRE. Settings found in tools>options>Ooo>Java. However, be warned:

 

  • Wizards don't work
  • The database functions don't work
  • You can't save in some of the funky formats like Pocket word.

 

(from http://www.linuxjournal.com/article/8308)

 

In the above figure, you can see that we selected the first expansion box and then clicked Memory with our mouse. This exposed the window you see in Figure 3. I changed the default values under the Graphics cache for Use for OpenOffice.org and Memory per Object. I increased the first value from 6 to 128MB. I also increased the second value from .5 to 20MB.

 

After clicking OK, I closed the word processor and reopened it two times. On each occasion, the application took less time to open. Under Ubuntu, I found that OO Writer opened in three seconds, and in Fedora it opened in less than six seconds. Previously, it took 30 and 26 seconds, respectively, for the word processor to launch.

 

Deviations:

 

Based on the previous how-to, we did not install:

 

 

To do list:

 

  1. Next working day agenda: icewm config files, finish up the biosoftware, install and run LCAT, fix automounting prob, burn alpha release, use checkinstall.
  2. Fix KDE dcop prob
  3. Clean up menus. Update artemis and sms2 which have been installed frm source.
  4. May want to remove mail icon from taskbar.
  5. Look for rox trash can.
  6. gaim smiley.
  7. include table of software
  8. bittorent client?
  9. reinstall installer according to how to.
  10. clean up the sys
  11. fortune
  12. rxvt memory leak?
  13. test out auto-apt updatedb and auto-apt update-local (from http://www.debian.org/doc/manuals/apt-howto/ch-search.en.html)
  14. List of known issues.
  15. Verify accuracy of how to.
  16. Find out what these means: sane* and not sane-utils?? /u
  17. Get the nice theme from here: http://www.ubuntuforums.org/showthread.php?t=171203
  18. Clean up the /etc/cron.* directories. Lots of cron jobs set to run (eg. cleaning up sendmail?) w/o checking if the service is actually running or not. Ends up with lots of <defunct> threads
  19. Check InitNG's ability to clean up <defuncts>

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