Installing GENESIS on Ubuntu requires executing the following major steps. Note: Installation requires administrator privileges.
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’):
echo ’joeuser ALL=(ALL) ALL’ >> /etc/sudoers
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):
echo ’joeuser ALL=(ALL) NOPASSWD:ALL’ >> /etc/sudoers
This script may be helpfull in installing these dependencies automatically.
This step is optional but strongly advised.
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:
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.
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:
neurospaces_upgrade --regex developer
and then perform a normal neurospaces_upgrade.
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:
Then download and install mtn-browse from http://www.coosoft.plus.com/software.html.
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:
neurospaces_uninstall --regex model-container
A special script uninstalls all the G-3 components but reinstalls the DeveloperPackage afterwards.
neurospaces_dev_uninstall --regex developer
Note that these commands leave the workspaces unaltered.