X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2Fbuilding.html;fp=doc%2Fbuilding.html;h=0000000000000000000000000000000000000000;hb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;hp=ecde4d88d016af127253153d08ddc950011ec08f;hpb=e6267883ffc25d76313c9e45967efe2c9e6d1d08;p=jalview.git diff --git a/doc/building.html b/doc/building.html deleted file mode 100755 index ecde4d8..0000000 --- a/doc/building.html +++ /dev/null @@ -1,99 +0,0 @@ - - - -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 -
- -