GENESIS: Documentation

Related Documentation:
GENESIS System

Developer Installation From Source On Mac OSX

The procedure for the installation of GENESIS on a Mac OSX is similar to that for a Linux build on a regular PC. The major difference is that it requires build tools for the Mac. These are somewhat hidden on disk 2 of the Mac OS installation disks. Installation requires administrator privileges. (Note: Some installation must be done from the Terminal). If you do not have administrator privileges you should contact your system administrator for help. The Terminal can be found in the Applications –> Utilities folder. For regular use of GENESIS it is convenient to place a Terminal in the dock for easy access. Installation requires executing the following major steps:

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

Prepare and upgrade the system software

Install the following packages:

• monotone-0.44: (or higher).
• Xcode Tools: The Apple Development Toolset. Xcode is available on Disk 2 of the Mac OSX installer set of DVDs under optional install. The package is called XcodeTools.mpkg. It is also available from the Apple Developer Website. In the latter case you will need a valid Apple ID to log in and access the developer page.
• Python: OS X comes with python, however it does not come with the headers and libraries so that you can build SWIG libraries. To get the development libs and headers, you must go to the official python site and download the installer. It is recommended that you stick with Python versions 2.5 and 2.6. The mac installer should update your execution path to allow you to execute your newly installed python. If it does not then you can add a line like this to your .bash_profile file:

  PATH="/Library/Frameworks/Python.framework/Versions/Current/bin:${PATH}"

  WARNING: The compilers available from MacPorts should NOT be used for installation (see below). Prior to installing the DeveloperPackage you should check which Perl libraries OSX uses with “which perl”. This should return /usr/bin/perl. If the response is /opt/local/bin/perl, there is a MacPorts installation of Perl. This is most easily corrected by removing the MacPorts path /opt/local/bin from your path in the .profile file in your home directory. To do this open the .profile file in an editor and convert the line (or similar):

  PATH=/opt/local/bin:/usr/local/bin:$PATH

  by removing /opt/local/bin to give:

  PATH=/usr/local/bin:$PATH

  Note: Only remove the MacPorts path and leave all others alone. If you do not make this change, running GENESIS may result in a bus error as the correct Perl libraries will not be found. It may also call MacPorts versions of build tools, which can result in some undesirable behavior.

  Note: Compiling from source will only produce executables and libraries for the host architecture. For example if you have a 64-bit system and 32-bit Perl, the compiled SWIG libraries will not load, giving an error similar to this:

  Note: For information on how to properly compile Universal Binaries for OS X, see this link.

  ./SwiggableHeccer.dylib: mach-o, but wrong architecture at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm

  so when compiling on a machine make sure that Perl, Python and all of their loadable modules and libraries are of the same architecture as the host machine.

• Install the following Perl dependencies via CPAN:
  • YAML
  • Digest::SHA
  • Inline
  • Parse::RecDescent
  • Expect (and its dependency perl-IO)
  • ExtUtils::MakeMaker
  • Data::Utilities
  • File::Find::Rule
  • Term::ReadLine

This can be done, for example, by entering the following at a terminal prompt:

Then at the cpan> prompt enter:

Download and Install the DeveloperPackage

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. (Note: If downloading via your browser, do not unpack the package during the download as it will be placed into its own subdirectory).

• Change to the directory where you downloaded the file.
• Unpack archive: “tar xfz developer-release-label.tar.gz”.
• Change to the directory with the content of the archive: “cd developer-release-label”.
• Configure the DeveloperPackage: “./configure”.
• Compile and install the DeveloperPackage: “sudo make install” (requires administrator privileges).

Install software packages

Once the above dependencies are installed source code can be pulled from the GENESIS repository and a build performed with the following commands:

1. neurospaces_create_directories
2. neurospaces_pull
3. neurospaces_update
4. neurospaces_configure
5. neurospaces_install (requires admin password)

Check if installation was successful

Once these have completed the installation can be tested with the following command:

• neurospaces_check >/tmp/check.out 2>&1

This will perform a series of regression tests and save the output to file. The output can be checked by typing “less /tmp/check.out”. Importantly, search for lines containing the string error_count that will indicate any inconsistencies with the installation.

Note: The running of tests is optional, but strongly advised.

Installation From Packages

Easiest method to install GENESIS 3 on Mac OSX is via installation packages available here. The packages install all compiled programs and scripts. However the prerequisite modules for Perl and Python must still be installed.

Required modules are listed in the GENESIS dependencies document. Note the above rule about macports still applies and the standard perl for Mac OSX at /usr/bin/perl should be the one invoked when pulling packages from CPAN.