# download
git clone http://source.jalview.org/git/jalview.git
# compile
-cd jalview
+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
# use launcher
-cd getdown/files
+cd ./build/getdown/files/11
java -jar getdown-launcher.jar . jalview
```
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`" or "`TEST`" 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
place to look for required files. If the selected channel type requires the getdown `appbase` to be a local
directory on the filesystem (instead of a website URL) then a modified version of the `getdown-launcher.jar` will
be used to allow this. The two versions of the `getdown-launcher.jar` can be found in `getdown/lib`.
+Note that the DEVELOP and RELEASE channels will normally use a getdown-launcher.jar that *does not* allow the
+`file://` scheme to be used in the appbase.
+
Some other variables used in the build process might also be set differently depending on the value of `CHANNEL`
to allow smooth operation of getdown in the given context.
-There are several values of `CHANNEL` that can be chosen, with a default of `LOCAL`. Here's what they're for and what they do:
+There are several values of `CHANNEL` that can be chosen, with no choice leading to a default of `LOCAL`.
+Here's what they're for and what they do:
-* `LOCAL`: This is for running the compiled application from the development directory.
+* `LOCAL`: This is for running the compiled application from the development directory and used by default.
It will set
- - `appbase` as `file://PATH/TO/YOUR/DEVELOPMENT/getdown/files/JAVA_VERSION`
- (e.g. `file://home/user/git/jalview/getdown/files/11`)
+ - `appbase` as `file://PATH/TO/YOUR/DEVELOPMENT/getdown/website/JAVA_VERSION`
+ (e.g. `file://home/user/git/jalview/getdown/website/11`)
- application subdir as `alt`
- Getdown launcher can use a `file://` scheme appbase.
+ - Compile jalview with `gradle getdown` or `gradle shadowJar`
+ - Run Jalview on the command line without using the installers with,
+ Using getdown, e.g. `java -jar ./getdown/files/11/getdown-launcher.jar ./getdown/files/11 jalview`
+ or using the shadowJar with, e.g. `java -jar ./build/libs/jalview-all-TEST-j11.jar`
* `BUILD`: This is for creating an appbase channel on the build server by an automatic or manually started build.
It will set
- `appbase` as `https://builds.jalview.org/browse/${bamboo_planKey}/latest/artifact/shared/getdown-channel/JAVA_VERSION`
gradle getdown -PCHANNEL=SCRATCH-my_test_version
```
+**New `CHANNEL` appearance features 2020-12-10**
+There are now differing cosmetics for different channels, including application icons, Getdown splashscreen,
+About splashscreen, Installer backgrounds, application name. This is controlled by the files in
+```
+utils/channels
+```
+In `utils/channels` there are different directories for the different channels. Currently there are directories for
+`default`, `develop`, `release`, `test-release`, `jalviewjs` and `jalviewjs-release`. If a specified `CHANNEL` is not one of `DEVELOP`, `RELEASE`, `TEST-RELEASE`, `JALVIEWJS`, `JALVIEWJS-RELEASE`
+then it will use the `default` directory.
+
+Inside the `utils/channels/<channelname>` directory are:
+- a file `channel_gradle.properties`. This will be used by the `build.gradle` script (i.e. any gradle build) to *override* the values found in `gradle.properties`.
+- an `images` directory used to store different images referred to in this channels's `channel_gradle.properties`.
+- a `resources` directory which is merged into the javliew.jar's own resources directory. Importantly it contains a `channel.props` file and another `images` dir which contains properties and images used by the application (in `jalview.util.ChannelProperties`), such as icon files or banner images, and the `app_name` property used as the display name for the application (e.g. "Jalview Develop") inside the application code. Please see the `getProperty` and `getImage` methods in `jalview.bin.ChannelProperties` to access these channel based resources.
+
+
#### JALVIEW_VERSION and the RELEASE file
Any Jalview build will include the value of JALVIEW_VERSION in various places, including the 'About' and Jalview Desktop window title, and in filenames for the stand-alone executable jar. You can specify a custom version for a build via the JALVIEW_VERSION property, but for most situations, JALVIEW_VERSION will be automatically configured according to the value of the CHANNEL property, using the `jalview.version` property specified in the RELEASE file:
- - `CHANNEL=RELEASE` will set version to jalview.version
- - `CHANNEL=TEST or DEVELOP` will append '-test' or '-develop' to jalview.version
+ - `CHANNEL=RELEASE` will set version to jalview.version.
+ - `CHANNEL=TEST or DEVELOP` will append '-test' or '-develop' to jalview.version.
+ - `CHANNEL=JALVIEWJS` will use the `channel.props` found in `utils/channels/jalviewjs` but otherwise uses `LOCAL` settings.
+ - `CHANNEL=JALVIEWJS-RELEASE` uses a symbolic link to `utils/channels/jalviewjs` but otherwise uses `RELEASE` settings.
It is also possible to specify a custom location for the RELEASE file via an optional JALVIEW_RELEASE_FILE property.
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