Basically, you need not particular operation after having downloaded the program file (AlignmentViewer.jar) — double click the icon (OSX or Windows) or type the java command (Unix) to invoke the program. See the chapter " The CGAT AlignmentViewer program "

However, in the default setting of the Java virtual machine (JVM), you will be likely to encounter a memory allocation error especially when aligning long sequences dynamically. To avoid this problem, you need to increase the size of the memory allocation pool for the JVM.

Figure 1. Increasing the size of the memory allocation pool of the JVM for AlignmentViewer on Windows XP


Copy the downloaded archive CGAT.tgz into an appropriate directory and extract files by tar command, which generates a directory named CGAT. Enter this directory and invoke a configuration script

tar cvfz CGAT.tgz
cd CGAT first asks you to set the CGAT_HOME environmental variable to the root of the generated directory tree (hereafter we call this directory $CGAT_HOME), and subsequently it sets several command paths and compiles some programs. saves the CGAT_HOME path in scripts etc/ for sh and bash and etc/cgat.csh for csh and tcsh. Before building the database or doing other operation, you must source the above script.

# in csh or tcsh
source etc/cgat.csh

# in sh or bash
. etc/
We recommend you to add this command to your .cshrc script (or .profile, .bashrc etc.) (in this case, you must use the absolute path rather than the relative path, of course).

The set up script tries to detect alignment programs available on the server machine and installs detected programs in the $CGAT_HOME/build/align directory. You might want to move some commands from the $CGAT_HOME/build/ directory or to remove some unnecessary commands manually.

Similarly, you might want to install manually some optional commands for collecting feature segments from the $CGAT_HOME/build/segment.opt directory. Note that in this case you must always set up by yourself (if you wanted), since currently the set up script does not try to check the availability of these commands automatically. Currently, the following commands are available: