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Mac OS X installation

How-to for installing Bikit under Mac OS X focusing on the use of the package manager Fink.

1. Python and Mac OSX

Mac OS X comes with Python pre-installed. However it is always a good idea to install your own version of Python (and leave the pre-installed version where it is as it is required by the OS). As Python 2.7.3 is the latest version in the 2.X branch go for this version which can be downloaded here -> Python 2.7.3. However the most hassle-free approach to obtain Python, Biskit and the required dependencies is using a package-manager. One of them is Fink and a Biskit package is available.

2. Installing Biskit (and Python) using Fink

The Fink package manager allows for the easy installation of Unix software under Mac OS X. As a prerequisite you need to download and install the Xcode developer tools from apple.

For users of 10.7 Lion: With the release of 4.3 Xcode became a full App and not only an installer, so if you update from previous versions this should be the last time you have to get the full package manually from the AppStore. Future releases should then be updated through the AppStore update functionality. But there are two important issues you have to pay attention to:

  1. After installing XCode 4.3 select the Components pane from Xcode->Preferences->Downloads and install the Command Line Tools

  2. Run:

    sudo xcode-select -switch /Applications/Xcode.app

to make sure that everything is pointed in the right place.

The next step would be to download Fink. We recommend getting the latest Fink source release. Following the instructions on the download page will install Fink and generate a new tree in the file system under /sw for installation and should also make this tree available in your shells PATH so you can directly access the installed packages from the command line.

After you have installed Fink (or have an existing installation already) you should open a Terminal windows and first issue the following command:

fink selfupdate

Biskit depends on Biopython but the Biopython fink package seems to be missing a dependency on flex. Therefore, first install flex:

fink install flex

Now we can install Biskit. To install the package for Python 2.7 run the following:

fink install biskit-py27

For Python 2.6 just substitute the py27 with py26. This will fetch Biskit and dependencies, compile and install them into the /sw tree. Python 2.5 is no longer supported with the fink package. If upgrading to 2.6 or 2.7 is no option, you have to install Biskit the "Do-it-yourself" way.

The following other packages are currently installed as dependencies:

There is currently no Fink package for PVM (Private Virtual Machine) and you are currently on your own (see the link) or you have to live with the fact that there is no parallel execution. However this is something currently being worked on, so stand by.

3. Installing Biskit the "Do-it-yourself" way

This is for the people who know what they are doing and how to do it. In general Biskit and the required dependencies should compile and install also under Mac OS X. You are referred to installation from source as described in the Short Instruction as a starting point.