+though you may need to fiddle with the `install4j` and `copyInstall4jTemplate` tasks
+in `build.gradle` file to point to your installation of *install4j* and also to bundled
+JREs if you want to bundle those into the installers.
+
+If you want more details, get in touch on our development mailing list <jalview-dev@jalview.org>.
+Sign up at <http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev>.
+
+
+## Building in Eclipse
+
+We develop in Eclipse, and support settings to develop and save Jalview source code
+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 2019-03
+version of Eclipse IDE for Java Developers which you can download from the Eclipse
+website: <https://www.eclipse.org/downloads/>
+
+Once installed, we also recommend installing several plugins from the Eclipse Marketplace.
+
+To do so, launch Eclipse, and go to Help->Eclipse Marketplace...
+
+Search for and install:
+
+1. Buildship Gradle Integration 3.0 (or greater)
+1. Groovy Development Tools 3.4.0 (or greater)
+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.
+However, you can install a working beta of TestNG for Eclipse by going to
+>
+Help->Install New Software...
+>
+and entering
+>
+`TestNG Eclipse Composite P2 Repo - http://beust.com/eclipse-beta`
+>
+into the *Work with* box and click on the *Add...* button.
+>
+Eclipse might pause for a bit with the word *Pending* in the table below at this point, but it will eventually list TestNG with
+a selection box under the *Name* column.
+>
+Select *TestNG* and carry on through the
+install process to install the TestNG plugin.
+
+After installing the plugins, it is a good to get Java 11 set up in Eclipse as the default JRE.
+
+To do this go to Preferences (Eclipse->Preferences in macOS, File->Preferences
+on Windows or Window->Preferences on Linux) and find
+
+Java -> Installed JREs
+
+If your Java 11 installation is not listed, click on
+
+*Add* -> Standard VM -> *Next*
+
+and enter the JRE home. You can browse to where it was installed. Give it a name (like "AdoptOpenJDK 11"). Select this JDK
+as the default JRE and click on *Apply and Close*.
+
+
+You can now import Jalview. It is important to import
+Jalview as a Gradle project (not as a Java project), so go to
+
+File->Import...
+
+find and select
+
+Gradle->Existing Gradle Project
+
+and then click on the *Next >* button.
+
+In the following options, it is the *Project Root Directory* you should set to be the
+`jalview` folder that git downloaded. Then you can click on the *Finish* button.
+
+
+## Gradle properties
+
+There are a lot of properties configured in `gradle.properties` which we strongly recommend
+being left as they are unless you have a specific problem with the build process.
+
+There are a few gradle properties you might want to set on the command line with the
+`-P` flag when building a version of Jalview with specific requirements:
+
+#### `JAVA_VERSION`
+This changes the *target* java bytecode version
+> NOTE that you will need to use a Java 11 (or greater) JDK Java compiler to build
+Jalview for any byte-code target version.
+
+Valid values are `11` and `1.8`.
+
+e.g.
+
+```bash
+gradle shadowJar -PJAVA_VERSION=1.8
+```
+
+When using `-PJAVA_VERSION=1.8` the libraries from `j8lib` (instead of `j11lib`) will be used in the compile
+and runtime classpath and also used in the `makeDist` build step. Where a Java version of `11` is used in folder and file names, it will
+instead use `1.8`. Also if you are building installer packages with *install4j* the
+package builder will look for JRE 1.8 bundles to package in the installers.
+
+> Note that continued development of Jalview will assume a Java 11+ runtime environment,
+the 2.11.0 release will run under a Java 1.8 JRE with a few minor features disabled.
+
+#### `CHANNEL`
+This changes the `appbase` setting in `getdown.txt` (`appbase` is where the getdown launcher
+looks to see if there's an updated file) to point to a particular Jalview channel or some other appropriate
+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`.
+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:
+
+* `LOCAL`: This is for running the compiled application from the development directory.
+ It will set
+ - `appbase` as `file://PATH/TO/YOUR/DEVELOPMENT/getdown/files/JAVA_VERSION`
+ (e.g. `file://home/user/git/jalview/getdown/files/11`)
+ - application subdir as `alt`
+ - Getdown launcher can use a `file://` scheme appbase.
+* `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/${bamboo_planKey}/latest/artifact/shared/getdown-channel/JAVA_VERSION`
+ Note that bamboo_planKey should be set by the build plan with `-Pbamboo_planKey=${bamboo.planKey}`
+ - application subdir as `alt`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `DEVELOP`: This is for creating a `develop` appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server.
+ It will set
+ - `appbase` as `http://www.jalview.org/getdown/develop/JAVA_VERSION`
+ - application subdir as `alt`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `SCRATCH-NAME`: This is for creating a temporary scratch appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server. This is meant for testing an over-the-air update without interfering with the live `release` or `develop` channels. The value of `NAME` can be any "word-character" [A-Za-z0-9\_]
+ It will set
+ - `appbase` as `http://www.jalview.org/getdown/SCRATCH-NAME/JAVA_VERSION`
+ - application subdir as `alt`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `TEST-LOCAL`: Like `SCRATCH` but with a specific `test-local` channel name and a local filesystem appbase. This is meant for testing an over-the-air update on the local filesystem. An extra property `LOCALDIR` must be given (e.g. `-PLOCALDIR=/home/user/tmp/test`)
+ It will set
+ - `appbase` as `file://${LOCALDIR}`
+ - application subdir as `alt`
+ - Getdown launcher can use a `file://` scheme appbase.
+* `TEST-RELEASE`: Like `SCRATCH` but with a specific `test-release` channel name. This won't become live until the actual getdown artefact is synced to the web server. This is meant for testing an over-the-air update without interfering with the live `release` or `develop` channels.
+ It will set
+ - `appbase` as `http://www.jalview.org/getdown/test-release/JAVA_VERSION`
+ - application subdir as `alt`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `RELEASE`: This is for an actual release build, and will use an appbase on the main web server with the main `release` channel name. This won't become live until the actual getdown artefact is synced to the web server.
+ It will set
+ - `appbase` as `http://www.jalview.org/getdown/release/JAVA_VERSION`
+ - application subdir as `release`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `ARCHIVE`: This is a helper to create a channel for a specific release version, and will use an appbase on the main web server with a specific `archive/JALVIEW_VERSION` channel name. This won't become live until the actual getdown artefact is synced to the web server.
+You must also specify an `ARCHIVEDIR` property that points to an earlier version of Jalview with a `dist` directory containing the required jar files. This should create a getdown structure and digest with the older jar files.
+ It will set
+ - `appbase` as `http://www.jalview.org/getdown/archive/JALVIEW_VERSION/JAVA_VERSION`
+ - application subdir as `alt`
+ - Getdown launcher cannot use a `file://` scheme appbase.
+* `ARCHIVELOCAL`: Like `ARCHIVE` but with a local filesystem appbase for local testing.
+You must also specify an `ARCHIVEDIR` property that points to an earlier version of Jalview with a `dist` directory containing the required jar files. This should create a getdown structure and digest with the older jar files.
+ It will set
+ - `appbase` as `file://PATH/TO/YOUR/DEVELOPMENT/getdown/website/JAVA_VERSION` (where the old jars will have been copied and digested)
+ - application subdir as `alt`
+ - Getdown launcher can use a `file://` scheme appbase.
+
+e.g.
+```bash
+gradle getdown -PCHANNEL=SCRATCH-my_test_version
+```
+
+#### `install4jMediaTypes`
+If you are building *install4j* installers (requires *install4j* to be installed) then this property specifies a comma-separated
+list of media types (i.e. platform specific installers) *install4j* should actually build.
+
+Currently the valid values are
+`linuxDeb`,
+`linuxRPM`,
+`macosArchive`,
+`unixArchive`,
+`unixInstaller`,
+`windows`
+
+The default value is all of them.
+
+e.g.
+```bash
+gradle installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive
+```
+
+To get an up-to-date list of possible values, you can run
+
+```bash
+perl -n -e 'm/^\s*<(\w+)[^>]*\bmediaFileName=/ && print "$1\n";' utils/install4j/install4j_template.install4j | sort -u
+```
+in the `jalview` root folder.
+
+
+## Enabling Code Coverage with OpenClover
+
+Bytecode instrumentation tasks are enabled by specifying 'true' (or just a non-whitespace non-numeric word) in the 'clover' property. This adds the 'openclover' plugin to the build script's classpath, making it possible to track code execution during test which can be viewed as an HTML report published at build/reports/clover/index.html.
+
+```gradle -Pclover=true test cloverReport```
+
+#### Troubleshooting report generation
+
+The build forks a new JVM process to run the clover report generation tools (both XML and HTML reports are generated by default). The following properties can be used to specify additional options or adjust JVM memory settings. Default values for these options are:
+
+##### JVM Memory settings - increase if out of memory errors are reported
+
+```cloverReportJVMHeap = 2g```
+
+##### -Dfile.encoding=UTF-8 is an essential parameters for report generation. Add additional ones separated by a space.
+
+```cloverReportJVMArgs = -Dfile.encoding=UTF-8```
+
+##### Add -v to debug velocity html generation errors, or -d to track more detailed issues with the coverage database
+
+```cloverReportHTMLOptions = ```
+
+##### -v for verbose, -d for debug level messages (as above)