GENESIS: Documentation

Related Documentation:
GENESIS System

Developer Installation Ubuntu (Karmic)

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

• Install the following packages using the Start Menu -> System Settings -> Add and Remove Software -> Software Management menu. Always follow the option to install additional dependencies.
  • libyaml-perl
  • libexpect-perl
  • libinline-perl
  • autoconf
  • automake
  • libc6-dev
  • libncurses5-dev
  • flex
  • bison
  • libperl-dev
  • patch
  • python-dev
  • python-yaml
  • swig
  • libreadline5-dev
  • libclone-perl
  • libterm-readline-gnu-perl
  • libxml-simple-perl
• monotone-0.45 (available as a statically linked binary from http://monotone.ca/)

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”.
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 recommendedthat you also install the dependencies of the G-Tube:

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

Studio

The following packages can optionally be installed to run the graphical part of the Studio:

• libgtk2-perl
• libgraphviz-perl
• sdl-perl
• xaw3dg (maybe also the developer package xaw3dg-dev).

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