cd jalview
gradle shadowJar
# run
-java -jar build/libs/jalview-all-11.jar
+java -jar build/libs/jalview-all-*-j11.jar
# and/or create launcher
gradle getdown
The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.
* Java 11 compliant JDK
-* gradle 5.2 or above
+* gradle 5.2 or above *(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)*
* git
> The versions and installation methods here are just suggestions (which we have tested
file. A default launching class (`MAIN-CLASS: jalview.bin.Launcher`) is specified in the `.jar`
manifest file (`META/MANIFEST.MF`) so a start class doesn't need to be specified.
-Build the shadow jar file in `build/lib/jalview-all-11.jar` with
+Build the shadow jar file in `build/libs/jalview-all-VERSION-j11.jar` with
```bash
gradle shadowJar
```
-and run it with
+
+__NB__ `VERSION` will be replaced with a version number or "`DEVELOPMENT`" depending on how the branch is set up.
+
+Run it with
```bash
-java -jar build/lib/jalview-all-11.jar
+java -jar build/libs/jalview-all-VERSION-j11.jar
```
Because no arguments are required, most OSes will associate a `.jar` file with the
`java` application (if this has been installed through the OS and not just a local
-unzip) as a `-jar` argument so you may find you can launch `jalview-all-11.jar`
+unzip) as a `-jar` argument so you may find you can launch `jalview-all-VERSION-j11.jar`
just by double-clicking on it)!
> The `shadowJar` task is not a requirement for any other task, so to build the shadow
We have made significant customisations to the `getdown` launcher which you can find
in `getdown/src/getdown`.
-> You don't need to build this afresh as the required `gradle-core.jar`
-and `gradle-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then
+> You don't need to build this afresh as the required `getdown-core.jar`
+and `getdown-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then
you'll need a working Maven and also a Java 8 JDK. Ensure the Java 8 `javac` is forefront
in your path and do
>
>cd getdown/src/getdown
>mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
>```
-> and you will find the required `.jar` files in `core/target/gradle-core-XXX.jar`
-and `launcher/target/gradle-launcher-XXX.jar`. The `gradle-core.jar` should then be copied
-to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `gradle-launcher.jar` only
+> and you will find the required `.jar` files in `core/target/getdown-core-XXX.jar`
+and `launcher/target/getdown-launcher-XXX.jar`. The `getdown-core.jar` should then be copied
+to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `getdown-launcher.jar` only
needs to be copied to `getdown/lib`.
>
>The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting.
getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`"
is defined here).
+The command line sequence for building and relocating the getdown artifacts can be executed as a script via `getdown/src/getdown/mvn_cmd`. Please make sure this script is kept up to date should the getdown build instructions change.
### Running tests
in our preferred style. We also support running the Jalview application, debugging
and running tests with TestNG from within Eclipse.
-To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03
version of Eclipse IDE for Java Developers which you can download from the Eclipse
website: <https://www.eclipse.org/downloads/>. Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.
1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
> At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
-as the latest released version does not install in Eclipse 2019-03.
+as the latest released version does not install in Eclipse 2020-03.
However, you can install a working release of TestNG for Eclipse by going to
>
Help->Install New Software...
If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
+__Before importing the cloned git repo you must create the Eclipse project files.__ You can do this by either running
+
+`gradle eclipse`
+
+or
+
+Unzipping the file `utils/eclipse/eclipse_startup_files.zip` in the base repo directory (`jalview`)
+
It is important to import
Jalview as a Gradle project (not as a Java project), so go to
git://source.jalview.org / jalview.git / blobdiff