3.12. Jemboss Installation: Platform-specific Concerns

3.12.1. MacOSX

These instructions refer to the 10.6 & 10.5 versions of MacOSX although similar principles apply to 10.3 and 10.4.


Also note that the EMBOSS developers can only realistically support the package on a virgin MacOSX installation using the installation methods described above. If you are having installation problems with any form of Jemboss provided by another project (e.g. MacPorts or Fink) then you should contact them for support. General Prerequisites

First, make sure you have acted on the prerequisites section for this operating system in the EMBOSS chapter. You will need Xcode, X11, X11SDK and PNG graphics. On top of that you will also need to have installed Java and the Java SDK. Depending on your version of MacOSX, not all of these may be installed by default so insert your MacOSX DVD (or look at the Xcode installation options) if necessary and do a custom installation and ensure that relevant check boxes are ticked.


With later versions of MacOSX, the Apple Xcode software should detect whether you have X11 installed and, if so, will install the X11SDK files. To be really sure of getting the latest versions of these packages then you will have to register as a developer at http://connect.apple.com. The process is simple, painless and free. When Running the Script

The Java location prompt should be answered with:


You should select PAM authentication for the latest versions of MacOSX.

When asked whether you wish to add any more configuration options, be sure to specify the location of your PNG installation e.g.


Prior to asking you for a password, the script may produce a warning message saying that it doesn't know what to set LD_PRELOAD to in the tomstart script. This warning can be ignored. For completeness you may wish to edit the tomstart script and change /usr/lib/libpam.so to /usr/lib/libpam.dylib.

Prior to automatic deployment you may be requested to edit the java.security file. This is located at:


Where version is your current version of Java e.g. 1.6.0. Typing:

java -version

in a terminal window will allow you to correctly choose which version to enter in the above file specification.

You may, however, notice that the java.security file already contains the required ssl provider line in which case no action needs to be taken.

3.12.2. IRIX General Prerequisites

Follow the prerequisites from the EMBOSS installation chapter. In addition you will need to download and install Java for Irix from the SGI website. The current version is 1.4.1. It installs into /usr/java2. As this is an older version of Java then you will need to download and install the Tomcat compatibility binaries on top of the Tomcat base binaries before running the Jemboss installation script. When Running the Script

You should set the CC environment variable before running the script e.g.

setenv CC cc


export CC=cc

depending on your shell.

When prompted for any extra configuration options, enter both the PNG and SGI compiler specification here (see EMBOSS chapter). For example:

--with-pngdriver=/usr/local -with-sgiabi=n32m4