On Unix and GNU/Linux the easiest way to run the program is to run the script called art in the Artemis installation directory (see the section called Getting and Installing Artemis in Chapter 1) like this:
If all goes well you will be presented with a small window with two menus. See the section called The Artemis Launch Window to find out what to do next.
Alternatively you start Artemis with the name of a sequence file or embl file eg:
Or if you have a sequence file and extra feature table files you can read them all with a command like this (the example file c1215.blastn.tab is the result of a BLASTN search against EMBL which has been converted to feature table format):
artemis/art artemis/etc/c1215.embl + artemis/etc/c1215.blastn.tab
Note that any number of feature files can be read by listing them after the plus sign. The "+" must be surrounded by spaces.
See the section called UNIX Command Line Arguments for Artemis for a list of the other possible arguments.
Here is an alternative way to run Artemis if the art script doesn't work for you:
java -classpath .:./lib/biojava.jar:./lib/jakarta-regexp-1.2.jar:./lib/jemAlign.jar -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain