X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2Fbuilding.html;h=ecde4d88d016af127253153d08ddc950011ec08f;hb=1dc67d212f52a92d7917fc9f4edd47d99b97c149;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/doc/building.html b/doc/building.html index e18e273..ecde4d8 100755 --- a/doc/building.html +++ b/doc/building.html @@ -1,18 +1,99 @@ + +Building Jalview from Source + + +

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 eclipse too, but NetBeans is a bit trickier). +
+   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 -sigalg SHA1withRSA -keyalg RSA -alias jalview
+ (you will have to answer some personal questions here) + 
ant makedist -DWebStartLocation="file://.pathtojalviewsource./dist" -Dapplication.codebase="*"
+

This should eventually generate a jalview.jnlp file in ./dist + along with a set of signed jars using the jalview key). In order to + test locally via webstart you'll now need to add 'file:/' to your + java webstart security exception list. Then:

+ 
javaws file://.pathtojalviewsource./dist/jalview.jnlp
+

Please remember to remove that entry afterwards, since it will leave + your system vulnerable to malicious code. +

+

+ Building the JalviewLite applet
+ The JalviewLite applet is compiled using a subset of the packages in + the src directory (specifically: MCView, and jalview.{datamodel, + analysis, appletgui, utils, schemes, api, structure}, and + com.stevesoft.*). Once compiled, these class files are obfuscated to + make the code run efficiently. To compile the applet Jar, use the + makeApplet task - optionally passing in a 'donotobfuscate' property to + the ant build (e.g. -Ddonotobfuscate=true) to disable obfuscation.

+ The ant target 'pubapplet' can be used to compile install the + jalviewApplet.jar and any dependent jars (under appletlib) into a copy + of the examples directory created under the outputDir build + property (which defaults to the 'dist' directory). +

+

+

using IDEs to build Jalview

+

The Jalview source distribution includes project definitions for + Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx + project files. These files should be sufficient to set up basic source + folders and build paths, but you will need to ensure that all .jar + files in the lib and appletlib directories are added to the build path + for your IDE project, and that the 'buildindices' target in Jalview's + build.xml is executed with the 'outputDir' ant property set to the + directory where the IDE expects to place compiled classes ('classes' + directory for eclipse, 'build/classes' for netbeans).

+

Note: It is generally not recommended that you distribute build + artefacts that were generated automatically via an IDE's own packaging + mechanism (e.g. Netbeans' executable Jar and dependent lib directory). + The hand-crafted ant build.xml is (currently) the only officially + supported method of building distributable versions of Jalview.

+
+Jalview development team +
+ +