GENESIS: Documentation

Related Documentation:
GENESIS System

Developer Installation Ubuntu (Precise)

Installing GENESIS on Ubuntu requires executing the following major steps. Note: Installation requires administrator privileges.

• Prepare and upgrade the system software.
• Download and install the DeveloperPackage.
• Install the software packages.
• Check if the installation was successful.

Prepare and upgrade the system software

Note on configuring sudo

When you install the G-3 developers release, it will create a “neurospaces_project” directory for development work in the home directory of the user doing the installation. This will hold subdirectories for each of the G-3 software components. Normally, you will want this user to be yourself, rather than root. In order to make it possible to install files in system directories, the install process makes use of sudo. Thus, you will need to install sudo and add yourself to the /etc/sudoers file. Ideally, you should use a tool called visudo to edit this file, in order to add your username. However, the easiest way is as root to do (for example for user ’joeuser’):

During the install process, you will be prompted for your password. However, when directing the output of an install or a “neurospaces_check” to a file, this can become a problem. The automated tests performed by a check take a long time, and it is easy to miss a password request and have it time out. If you are on a secure single-user system, you may wish to avoid the password check and set it with (for example):

Packages to Install

• Install the following packages using the Start Menu. Type ’software’ in the edit box of the Start Menu and use any of the proposed software package management systems. We have used the management system called ’Synaptic’ (if ’Synaptic’ is not installed, it can be installed using the ’Muon’ program available from the Start Menu). Always follow the option to install additional dependencies.
  • libyaml-perl
  • libexpect-perl
  • libinline-perl
  • libfile-find-rule-perl
  • libdigest-sha-perl
  • libdevel-ptkdb-perl
  • libreadline-dev
  • autoconf
  • automake
  • make
  • libc6-dev
  • libncurses5-dev
  • flex
  • bison
  • libperl-dev
  • patch
  • python-dev
  • python-yaml
  • swig
  • libclone-perl
  • libterm-readline-gnu-perl
  • libxml-simple-perl
  • latex2rtf
  • biblatex
  • tex4ht
  • texlive-humanities
  • rst2pdf
  • unrtf
  • jodconverter
  • monotone
  • libgtk2-perl
  • libgraphviz-perl
  • libsdl-perl
  • xaw3dg
  • libintl-perl

This script may be helpfull in installing these dependencies automatically.

Download and Install the DeveloperPackage

1. Download the latest version of the DeveloperPackage, available from the GENESIS package archive. It is called developer-release-label.tar.gz, where release-label is the current release identifier.
2. Change to the directory where you downloaded the file.
3. Unpack the archive by typing “tar xfz developer-release-label.tar.gz”.
4. Change to the directory with the content of the archive by typing “cd developer-release-label”.
5. Configure by typing “./configure”. If this step fails, it is likely due missing dependencies. If you let us know what dependencies were missing for you, we can update this page, and avoid installation problems for other people.
6. Compile by typing “make”.
7. Install by typing “sudo make install”.

Install software packages

1. Use the installer script to create the correct directory layout by typing “neurospaces_create_directories”.
2. Pull the archives of the source code by typing “neurospaces_pull”.
3. Update the source code in the working directories by typing “neurospaces_update”.
4. Generate make files by typing “neurospaces_configure”.
5. Compile and install the software by typing “neurospaces_install”.

Check if the installation was successful

This step is optional but strongly advised.

• Run tests of all the packages and save tester output to a file by typing “neurospaces_check >/tmp/check.out 2>&1”.
• Check the output by typing “less /tmp/check.out”. Importantly, search for lines containing the string error_count.

Optional Dependencies

G-Tube

As the G-Tube is becoming more mature as the official G-3 GUI, it is strongly recommended that you also install the dependencies of the G-Tube:

• mercurial
• python-numpy
• python-wxgtk2.8
• python-wxglade

Neurospaces Studio Testing (Optional)

After successful installation, issue the shell command “neurospaces cells/purkinje/edsjb1994.ndf --gui” to check that the graphical component works of the Neurospaces Studio are working correctly.

Upgrading an Installation

While G-3 is under rapid development, it is important to frequently upgrade your installation with the “neurospaces_upgrade” command. As with “neurospaces_install”, this is performed in your home directory, with the output and error messages directed to a log file.

If Error messages are found in the upgrade log file, they may indicate a new dependency that needs to be installed. When upgrading an older version, sometimes the installation of a particular software component will fail, but repeating the “neurospaces_upgrade” will result in a successful installation. If there have been changes in the DeveloperPackage that prevent a successful upgrade, you may update this package first, by using the command:

and then perform a normal neurospaces_upgrade.

Optional: Browsing Version History

It may be useful to core developers to browse recent version history and inspect specific changes implementing new functionality. G-3 uses both monotone and mercurial for version control.

To browse the change history stored in a (local) monotone repository, install the following dependencies:

• libgtk2-sourceview2-perl
• meld

Then download and install mtn-browse from http://www.coosoft.plus.com/software.html.

Uninstalling G-3 Components

The script “neurospaces_uninstall” will uninstall G-3 but leave the workspaces unaltered. The script will also uninstall the developer package, so it can best be used with a “–regex” option to select the component you want to uninstall:

A special script uninstalls all the G-3 components but reinstalls the DeveloperPackage afterwards.

Note that these commands leave the workspaces unaltered.