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en:install:tree_structure [2013/06/27 08:54] – [Base Installation] foisysen:install:tree_structure [2021/05/29 15:35] (current) – external edit 127.0.0.1
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 +====== 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>