GENESIS: Documentation

Related Documentation:

Developer Installation Fedora 12 and Higher


The documentation below gives specifics for installing GENESIS 3 on Fedora Linux versions 12 and higher. It also contains some more general information that will later be included in the general Developer Installation documentation.

The documentation GENESIS Developer Installation gives an overview and prerequisites for the construction of a GENESIS 3 (G-3) development environment. Note that this involves a lot more steps than installing a User Installation, because of the software tools required for G-3 development. If you do not plan to check in changes to the software, it is not necessary to create a monotone passphrase.

Installation Steps

Installing GENESIS on Fedora 12 requires executing the following major steps. Note: Installation requires administrator privileges.

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’):

        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

Prepare and upgrade the system software

Download and install the DeveloperPackage

  1. You can download the DeveloperPackage from the GENESIS package archive. It is called developer-release-label.tar.gz, where release-label is the current release identifier.
  2. For the most up to date version of the DeveloperPackage, you can download the latest snapshot from the development repository here.
  3. Change to the directory where you downloaded the file.
  4. Unpack the archive by typing “tar xfz developer-release-label.tar.gz”.
  5. Change to the directory with the content of the archive by typing “cd developer-release-label.
  6. Configure by typing “./configure”.
  7. Compile by typing “make”.
  8. Install by typing “sudo make install” (requires administrator privileges).

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”.

Checking for installation errors

A first attempt at a developer installation of G-3 may fail because one of the required software dependencies was not installed. It is therefore a good idea to capture the output and all error messages resulting from the “neurospaces_install” command into a log file. For example when using the bash shell:

    neurospaces_install > install.log 2>&1

or for csh or tcsh:

    neurospaces_install > & ! install.log

You may observe the progress in another terminal window in your home directory with:

    tail -f install.log

This is particularly useful if you expect to be prompted for a password by sudo. Once the installation has completed, look for errors in the log file with “grep Error install.log”. A closer examination may show a missing dependency.

Enabling G-Tube

The GUI interface for G-3, g-tube is still under development, so its installation is disabled in the developer package by default. To perform an install with g-tube, give the commands:

        neurospaces_create_directories --enable g-tube  
        neurospaces_init --regex g-tube --enable g-tube  
        neurospaces_pull --enable g-tube  
        neurospaces_update --enable g-tube  
        neurospaces_install --enable g-tube

Check if installation was successful

This step is optional.

Updating the 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:

    neurospaces_upgrade --regex developer

and then perform a normal neurospaces_upgrade.