Building Jalview from Source

You will need the following (hopefully):

With any luck, after setting your paths and JAVA_HOME correctly, you just need to change to the Jalview directory and run ant (this works from JBuilder and eclipse too).
   ant

Building a webstart version of jalview

Jalview depends on several libraries contained in the libs directory of the distribution. In order to access them, they must all be signed jars - using the same jarsigner key as jalview itself. There is a build target in ant to make the signed jar files in a directory called dist. But first you need to make your own key:

Making your own key

The ant 'makejars' target assumes that a keystore exists in a directory 'keys'. To make a key accessible using the default settings in the build.xml file then make the keys directory and add the jarsigner key with the following :

mkdir keys
keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
-storepass alignmentisfun -alias jalview
 (you will have to answer some personal questions here)
ant makejars
 (should eventually generate a Jalview.jnlp file 
  in ./dist along with a set of signed jars using the jalview
  key)

Jalview development team