Impilo specific modifications to the base system

• As starting point, I use a CD-ROM image of Ubuntu's Minimal installer that I want to use; I use this ISO file as boot disk for my newly created VirtualBox's VM.
  • Use the latest LTS version (as of 06/2-13, it is Ubuntu 12.04).
  • As a first username/password combination, I use bioubuntu and bioubuntu.

• After the VM has booted from the image and the installation process has completed, I choose the following options for a minimal Impilo installation: Ubuntu Basic Server,OpenSSH Server.
  • For more functionality, you cam also install the LAMP Server meta-package. As password for the MySQL root user, I use bioubuntu/bioubuntu.
  • Of course, you need to change this ASAP if you are planning to build a production system from the basic Impilo VM. You have been warned!!

• Once the virtual machine has restarted, you need to install some extra packages so that the local documentation wiki as well as some remote access tools can work:

// If you have not install the LAMP Server meta-package
% sudo apt-get -y --no-install-recommends install apache2 php5 mysql-client
 
// If you have install the LAMP Server package, only PHP is necessary.
% sudo apt-get -y --no-install-recommends install php5

• Using the minimal installer insures that you have the latest version of everything

Because I wanted not to be too “unique”, I decided to put all the Impilo-specific content under /opt/bio. Inside this folder, you will find:

• /opt/bio/data
  All relevant biological data files used by Impilo (for example, BLAST database files).

• /opt/bio/docs
  All of the documentation created for Impilo, including this wiki. Consult these necessary instructions for the Impilo-specific Apache configuration of the virtual host.

• /opt/bio/scripts
  All of the scripts to automate the installation of Impilo on a new VM (more to come actually . We are aiming for automatic installs).

• /opt/bio/sources
  Where all the bioinformatics apps live.

• Remove the comment from this line to allow colors in the console:

#force_color_prompt=yes

becomes

force_color_prompt=yes

• Modify the following block to shorten filesystem navigation display and remove the default green color as default for the user prompt:

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi

becomes

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\[\033[01;34m\]\W\[\033[00m\]\$'
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
fi

• Finally, remove the comment for this line to highlight grep-filtered content:

#alias grep='grep --color=auto'

becomes

alias grep='grep --color=auto'

• After this, copy this file over the /home/bioubuntu to give these abilities to the bioubuntu user. All new users will have it by default.

As a user logs onti an Ubuntu server, the script that creates the session for this user reads the files located under /etc/profile.d to set various parameters for the sessions. This is where wu will put a file specific to Impilo, /etc/profile.d/impilo.sh, which will specify the environment variables specific to Impilo:

% sudo touch /etc/profile.d/impilo.sh