Building Jalview from Source

You will need the following (hopefully):

Java development kit (we used JDK1.5SE but JDK1.6 will work too, and maybe even jikes).
Ant (we think 1.5.4 is quite sufficient to use the simple build file supplied).

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 'makefulldist' 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 makedist
 (should eventually generate a Jalview.jnlp file
  in ./dist along with a set of signed jars using the jalview
  key)

Jalview development team