(Please email us at ) with questions or comments about downloading Mesquite).
Requirements: JRE or JDK 1.1.8 or better (java.sun.com). Recommended: 1.4.1 or higher. (It is best to get Sun's Java VM; Mesquite does not run on some third-party virtual machines.) See notes on the support page, especially regarding issues with window and dialog size and placement.
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It will create a directory called "Mesquite_Folder" in which all the relevant files reside. To start Mesquite, execute the run_mesquite.sh script from the command line:
path/to/Mesquite_Folder/run_mesquite.shYou may have to set this to executable before running. This script should automatically identify your java installation and run Mesquite. If you have trouble, you may need to set your JAVA_HOME environment variable. In the uncommon case that you want a java VM to run Mesquite that is different from the VM identified in JAVA_HOME, you may set the MESQUITE_JAVA_HOME environment variable.
If the current user directory is not the Mesquite_Folder, and Mesquite has not been run before, Mesquite may ask you to find the file "manual.html" which resides in the Mesquite_Folder/docs/mesquite/ directory. This will help Mesquite find and remember where its files are.
Once Mesquite has finished loading, go to the File menu to open a file. To start mesquite with one or more nexus files open, pass the file names as arguments to run_mesquite.sh, e.g.
path/to/Mesquite_Folder/run_mesquite.sh path/to/file1.nex path/to/file2.nex
java -cp path/to/Mesquite_Folder mesquite.Mesquite
where path/to/Mesquite_Folder could be replaced by whatever is the path to the Mesquite_Folder. On some systems the java virtual machine is started by "jre" instead of "java", and thus the command would be:
jre -cp path/to/Mesquite_Folder mesquite.Mesquite
Depending on your configuration, you may need to give the explicit path to the java virtual machine, as in:
/usr/java/jre1.4.2/bin/java -cp path/to/Mesquite_Folder mesquite.Mesquite
If you've changed the name of Mesquite_Folder to, for instance, "Mesquite1", you may need to use a command like:
/usr/java/jre1.4.2/bin/java -cp path/to/Mesquite1 mesquite.Mesquite
If you've had to do all this because the shell script isn't working, please let us know what happened, and what you did to make Mesquite work. That way, we can make it easier for the next person.
Mesquite attempts to place windows in particular places on the screen for ease of use, using standard Java calls. Some window managers override this, resulting in haphazard placement of windows. You may need to change your window manager if this sort of thing is happening.
More details of issues of using Mesquite under Linux/UNIX are described in the Support page.