Developing with the Jalview source [ was Re: Hello Jalview team please help me to start Jalview. ]

Dear. sir or madam


Hello Seho.

It’s great to hear that you’d like to participate in Jalview development! I suggest before you go any further, that you sign up over at and register for the jalview-discuss and developer email lists (details at ).

To get started with Jalview’s source, try out the following:

i. Unpack the tar.gz ball somewhere (either into your eclipse workspace or to some other directory).
ii. Use the ‘Import existing projects’ option from the File->Import menu. If you unpacked the tarball in your workspace, then make sure to not tick the ‘copy project into workspace’ option.

Alternatively, if you are serious about developing Jalview, then:
i. Use the eclipse git client to clone the git repository at
ii. Switch to the ‘Jalview_Release_2_8’ Branch (or Jalview_Release_2_8_1_Branch if you’d like to work on the next version).
iii. Import the project from the cloned repository. (once you’ve done this, you can switch branches directly from the project).

  1. Make sure the project is building correctly

If you see any ‘!’ symbols next to your project, these indicate the project configuration is not right. Usually, you only need to fix the build paths:

i. Everything under lib needs to be listed under ‘Referenced libraries’

ii. Your project builders should include an ‘ant’ build step which executes the ‘prepare’ target. This will ensure that all Jalview’s resources are on the runtime classpath. You can do this manually by 'Run…'ning the build.xml file and picking the ‘prepare’ target from the list of possible targets.

iii. The applet source will only compile when you have the ‘plugin.jar’ on your build path. Most likely, when you browse to the Jalview project’s build classpath, you’ll see a user library called ‘plugin.jar’ which has a warning next to it (if not, use the button to create a new user library). You’ll need to edit the library to make sure it points to the ‘plugin.jar’ on your system. Normally this jar is located inside the lib directory of your JRE or JDK.

Let me know how you get on !

On 14/10/2013 20:41, Seho Choi wrote: