You can specify an arbitrary builder on an Eclipse project, and order the builder so that it is executed before the Java builder is run.
To define the new builder, open the project properties (right click->Properties or alt-enter), select Builders then New.... Select Program, then in the dialog configure the builder (hopefully you know what needs to be done here) and select OK. Back in the Builders page you can then select your new builder and select Up until it is before the Java Builder
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