Apple released the new version of their operating system, OS X 10.7 Lion, on July 20, 2011. Lion is a major overhaul of OS X. This page lists the known differences between Lion and previous versions of OS X that are relevant to using Practical Computing for Biologists with a Mac. It also includes solutions for getting things to work smoothly.
- XCode tools, which includes the compiler tools needed to install some software, is not included with Lion. But it can be downloaded for free from the Apple Mac App Store . After you have installed XCode, you need to install the command line tools as well. To do this, go to XCode Preferences, select the Downloads pane, and click the Install button next to Command Line Tools.
- The Java Runtime Environment (JRE) is no longer installed by default on Lion. This software is needed to run programs written in the language Java. Though the book does not cover Java programming, some of the GUI programs discussed in the book, including ImageJ, the MySQL Workbench, and others, do have Java code and need the JRE to run. To install the JRE, open the Java Preferences program in the Utilities folder in the Applications folder. You will be prompted to install "a Java runtime".
- We are not aware of any problems running MySQL Community server 5.5.15 on Lion, even though Lion compatibility is not mentioned on the downloads page. The MySQL DMG installer works fine when following the instructions in the book.
- To install the MySQLdb Python module, follow the tips in this thread. In short, use
pipl, and then use
- Python version 2.7 is installed by default, and
numpyis pre-installed for you!
- Do not install the 32 bit version of MySQL- stick with the 64 bit version or you will end up with problems connecting to mysql from python.
- To prevent the Terminal from reopening In a saved state with your last window of commands, paste this command (as one line) in a Terminal window, then quit and restart the program twice:
defaults write com.apple.Terminal NSQuitAlwaysKeepsWindows -bool false