====== Impilo specific modifications to the base system ======

===== Base Installation =====

  * As starting point, I use a CD-ROM image of [[https://help.ubuntu.com/community/Installation/MinimalCD|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:

<code bash>
// 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
</code>


  * Using the minimal installer insures that you have the latest version of everything :-)

===== File system tree structure used by Impilo =====

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 [[apache_config_impilo|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.
 

===== Modifications of specific files of the base system ===== 

==== Modification to /etc/skel/.bashrc ====

  * Remove the comment from this line to allow colors in the console:
<code bash>
#force_color_prompt=yes
</code> 

becomes

<code bash>
force_color_prompt=yes
</code> 

  * Modify the following block to shorten filesystem navigation display and remove the default green color as default for the user prompt:
<code bash>
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
</code>

becomes

<code bash>
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
</code>

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

<code bash>
#alias grep='grep --color=auto'
</code>

becomes

<code bash>
alias grep='grep --color=auto'
</code>

  * 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.

==== Creating the /etc/profile.d/impilo.sh file ====

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:

<code>
% sudo touch /etc/profile.d/impilo.sh
</code>