Misc links

From Shiu Lab

Contents 1 Linux/Unix/Cygwin related 1.1 Unix tricks 1.2 About X 1.3 Rock cluster 1.4 Samba 2 InterProScan 3 R/Bioconductor 4 Other bioinformatics software 5 PDF 6 Rock cluster 7 Windows annoyance 8 Weird stuff 8.1 Jokes

Linux/Unix/Cygwin related

Unix tricks

• Advanced Bash-Scripting Guide: An in-depth exploration of the art of shell scripting
• Rid of ^M: The problem with switching back and forth from Unix and Windows...
• SSH login script
• Linux file find: A useful site with lots of tutorial on linux.

• VIM
  • Best of VIM tips:
  • Vim cheatsheet
  • Tabstop: in home dir find .exrc, add the line set tabstop=4.

• How to deal with 'argument list too long'
• VI cheatsheet
• All about path
• Unix find
• GNU software packages
• What to do when the unix screen freeze: Frequently happen when ctrl-s is pressed accidentally.
• Linux Home Networking Howto on Firewall

About X

• Cgwin/X: a port of the X Window System to the Microsoft Windows family of operating systems.
• Cygwin/X setup: A tutorial from Old Dominion University.
• KDE on Cygwin: Check here for installation instruction.
• icewm: another window manager.
  • Requires: readline, gettext-devel, imlib, libjpg6b, glib2, x-org-x11-devel, libiconv.
  • Installation instruction.
  • Found this ./configure setting from here:

./configure --disable-xinerama --disable-xfreetype --disable-nls --disable-shape --disable-xrandr --without-imlib --enable-corefonts

• OpenBox:
  1. Documentations
  2. ObConf: Configuration utility. Some info on installation in cygwin. Need pkg-config
• Ical: X-based free calendar

Rock cluster

• Adding user

useradd username 
passwd username 
rocks-user-sync 

• Mailing list

Samba

• Samba setup in linux

• Add new users
  1. Switch to root in calculon
  2. run: /usr/local/bin/samba/bin/smbpasswd -a username
  3. restart smbd: /etc/rc.d/init.d/smb restart

• Troubleshoot
  • Samba and IPTables: make sure the ports are open for samba.
  • Samba checklist
  • Samba testing
  • ITworld article
  • No service fix
  • NT_STATUS_WRONG_PASSWORD error fix

InterProScan

• Installation document. Run into multiple problems trying to run it on calculon.
• Required perl modules need to be installed on the head and every computing nodes:

perl -MCPAN -e shell
# May need to update CPAN
install Bundle:CPAN
# in our case the following need to be installed
install XML::Parser
install Mail::Send
install IO::Scalar
install IO::String
install URI::Escape

R/Bioconductor

Other bioinformatics software

• Fixed blastpgp segmentation fault

PDF

• Optimize PDF size

Rock cluster

• Documentation
• Short FAQs: including info on passwordless ssh.
• Add user

useradd <newuser>
passwd <newuser>
make -C /var/411

Windows annoyance

• Remove messenger ads
• Windows application default change:

NT/W2K/XP's default directory for installing applications is the \Program Files folder (at least for English language version of NT/Windows 2000/XP). To change the default application installation folder:

Hive: HKEY_LOCAL_MACHINE
Key: Software\Microsoft\Windows\Current Version
Name: ProgramFilesDir
Type: REG_EXPAND_SZ
Value: C:\Program Files default 

• Modify restart prompt frequency
• Deal with MS Word nuisance
• MS Excel relative references
• Windows XP performance tip

Weird stuff

• Acronym finder
• Google analytics
  • Info on where to add the tracking codes in Mediawiki]

Jokes

• M&M