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Building Jalview from Source

tl;dr

# download
git clone http://source.jalview.org/git/jalview.git
# compile
cd ./jalview
gradle shadowJar
# run
java -jar build/libs/jalview-all-*-j11.jar

# and/or create launcher
gradle getdown
# use launcher
cd ./build/getdown/files/11
java -jar getdown-launcher.jar . jalview

Setting up

To get set up using only the Eclipse IDE (https://www.eclipse.org/) then please see the section Setting up in Eclipse IDE

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 (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 so are known to work). If you need or wish to use different implementations (particularly you might need a bespoke JDK if you are on an exotic architecture) then the general build instructions should work with any gradle 5+. You should be able to compile the bytecode with any JDK Java 11+. The resulting bytecode (in particular the shadow jar) should be runnable in any JRE Java 1.8+. Remember that because Jalview and the getdown launcher are Java bytecode you can build on one system where you might have gradle, and run on another where you don’t (JRE 1.8+ required).

Java 11 compliant JDK

All platforms

We recommend obtaining an OpenJDK JDK 11 (since 11 is the long term support release) from AdoptOpenJDK: https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot, either the Installer or .zip/.tar.gz variants whichever you prefer (if you’re not sure, choose the Installer).

Alternative/CLI install of AdoptOpenJDK 11

You can also install adoptopenjdk11 using either brew (macOS), choco (Windows) (see the section on gradle and git for more informaiton on brew and choco) or yum or apt (Linux):

alternative for MacOS and Homebrew

brew tap adoptopenjdk/openjdk
brew cask install adoptopenjdk11

alternative for Windows and Chocolatey

choco install adoptopenjdk11

alternative for Linux with yum/apt

see https://adoptopenjdk.net/installation.html#linux-pkg

gradle and git

You should be able to install the latest (or sufficiently recent) versions of gradle and git using your OS package manager.

MacOS

we recommend using brew, which can be installed following the instructions at https://brew.sh/. After installing brew, open a Terminal window and type in (using an Administrator privileged user):

brew install gradle git

or if you aready have them installed but need to upgrade the version:

brew upgrade gradle git

Windows

we suggest using the Chocolatey package manager. See install instructions at https://chocolatey.org/, and you will just need

choco install gradle
choco install git

Alternatively, you could install a real bash shell and install both gradle and git through apt-get. See https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/ for how to install the ubuntu bash shell in Windows 10.

Another alternative would be to install them separately. For gradle follow the instructions at https://gradle.org/install/, and for git here are a couple of suggestions: Git for Windows https://gitforwindows.org/. Getting the individual installs working together on the command line will be trickier so we recommend using Chocolatey or bash.

Linux

this will depend on which distribution you’re using.

For Debian based distributions (e.g. Mint, Ubuntu, Debian)

run

 sudo apt-get install gradle git

for RPM-based distributions (e.g. Fedora, CentOS, RedHat)

run

sudo yum install gradle git

If you have some other version of linux you’ll probably be able to work it out!

Downloading the Jalview source tree

This can be done with git. On the command line, change directory to where you want to download Jalview’s build-tree top level directory. Then run

git clone http://source.jalview.org/git/jalview.git

You’ll get some progress output and after a minute or two you should have the full Jalview build-tree in the folder jalview.

What’s in the source tree?

Jalview is a mature product with its codebase going back many years. As such it doesn’t have a folder structure that most new gradle projects would have, so you might not find everything in the place you might expect. Here’s a brief description of what you might find in the main folders under the jalview tree.

Within the jalview folder you will find (of possible interest):

Note that you need a Java 11 JDK to compile Jalview whether your target build is Java 1.8 or Java 11.

Building Jalview

You will need to have the Java 11 javac in your path, or alternatively you can configure gradle to know where this is by putting

org.gradle.java.home=/path_to_jdk_directory

in the gradle.properties file.

You may want to see some of the other properties you can change at the end of this document.

Minimal Jalview Build

To compile the necessary class files, just run

gradle compileJava

to compile the classes into the classes folder. You should now be able to run the Jalview application directly with

java -cp "classes:resources:help:j11lib/*" jalview.bin.Jalview

You can also run with an automatic large memory setting (which will set the maximum memory heap of the Jalview JVM to 90% of your local physical memory) and docked icon setting (if possible in your OS) with

java -cp "classes:resources:help:j11lib/*" jalview.bin.Launcher

You must use just “j11lib/*” and not “j11lib/*.jar” as this is a special Java classpath argument wildcard interpreted by java, not a shell expansion wildcard interpreted by the shell.

Note that jalview.bin.Launcher is a simplified launcher class that re-launches jalview.bin.Jalview with the same JRE (not the same JVM instance), classpath and arguments, but with an automatically determined -Xmx... memory setting if one hasn’t been provided.

Jalview in a Jar File

To package the classes, resources, and help into one jar, you can run

gradle jar

which assembles the Jalview classes and resources into dist/jalview.jar

To run this, use

java -cp "dist/jalview.jar:j11lib/*" jalview.bin.Jalview

Distributed Jar Files

To simplify this, all required .jar files can be assembled into the dist folder using

gradle makeDist

which puts all required jar files into dist so you can run with

java -cp "dist/*" jalview.bin.Jalview

Single shadow Jar File

The shadow jar file is a single .jar that contains all required classes and resources from jalview.jar and all of the supporting libraries in j11lib/*.jar merged into one .jar archive 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/libs/jalview-all-VERSION-j11.jar with

gradle shadowJar

NB VERSION will be replaced with a version number or “DEVELOPMENT” or “TEST” depending on how the branch is set up.

Run it with

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-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 jar file you must specify the shadowJar task.

The shadow jar file represents probably the simplest way to distribute the Jalview application to machines that already have a Java 11 installed, although without the many and compelling benefits of the getdown launcher.

Building the getdown launcher

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’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 needs to be copied to getdown/lib.

The mvn command should ideally include the -Dgetdown.host.whitelist=*.jalview.org setting. This, and the necessary file copying commands, can be found in getdown/src/getdown/mvn_cmd.

To assemble Jalview with getdown use the following gradle task:

gradle getdown

This puts all the necessary files to launch Jalview with getdown into getdown/website/11/. This could be treated as the reference folder for getdown, which is where a getdown launcher will check to see if the Jalview application files it has are up to date, and download if they aren’t or it simply doesn’t have them.

A minimal getdown-launcher can be found in getdown/files/11/ which checks its up-to-date status with (the absolute path to) getdown/website/11/.

This can be launched with

java -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview

We’ve already met the -jar file.jar arguments. The next argument is the working folder for getdown, and the final argument, “jalview”, is a getdown application id (only “jalview” is defined here).

Running tests

There are substantial tests written for Jalview that use TestNG, which you can run with

gradle test

These normally take around 5 - 10 minutes to complete and outputs its full results into the tests/ folder. A summary of results should appear in your console.

You can run different defined groups of tests with

gradle test -PtestngGroups=Network

Available groups include Functional (default), Network, External.

Excluding some tests

Some of Jalview’s Functional tests don’t pass reliably in all environments. We tag these tests with a group like ‘Not-bamboo’ to mark them for exclusion when we run tests as part of continuous integration.

To exclude one or more groups of tests, add them as a comma separated list in testngExcludedGroups.

gradle test -PtestngExcludedGroups=Not-bamboo

Installer packaging with install4j

Jalview is currently using install4j https://www.ej-technologies.com/products/install4j/overview.html as its installer packaging tool.

If you have a licensed installation of install4j you can build Jalview installers by running

gradle installers

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.

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.

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. 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 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 and used by default. It will set
  • 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/${bamboo_planKey}/latest/artifact/shared/getdown-channel/JAVA_VERSION Note that bamboo_planKey should be set by the build plan with -Pbamboo_planKey=${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.

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=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.

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.

gradle installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive

To get an up-to-date list of possible values, you can run

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)

cloverReportXMLOptions =

Note do not forget to include the -Dfile.encoding=UTF-8 option: this is essential for some platforms in order for Clover to correctly parse some Jalview source files that contain characters that are UTF-8 encoded.

Setting up in Eclipse IDE

Installing Eclipse IDE

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 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.

Once Eclipse is installed, we also recommend installing several plugins from the Eclipse Marketplace.

Some of these should already be installed with the Enterprise Java Developer package:

1. Buildship Gradle Integration 3.0 (or greater)
2. EclEmma Java Code Coverage
3. Egit - Git Integration for Eclipse

To install the others, launch Eclipse, and go to Help->Eclipse Marketplace…

Search for and install:

1. Groovy Development Tools 3.4.0 (or greater)
2. Checkstyle Plug-in (optional)
3. 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 2020-03. However, you can install a working release of TestNG for Eclipse by going to

Help->Install New Software…

and entering

TestNG Release - https://dl.bintray.com/testng-team/testng-eclipse-release

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, check that Java 11 is set up in Eclipse as the default JRE (see section Java 11 compliant JDK).

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 is 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.

Importing Jalview as an Eclipse project

Importing an already downloaded git repo

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

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.

Using Eclipse IDE to download the git repo

If you don’t have git as a command line tool or would prefer to work entirely within Eclipse IDE then Eclipse’s eGit plugin can set up a git repo of the jalview source. Go to

File->Import…

Find and select

Git->Projects from Git

and then click on the Next button.

Then select Clone URI and click on Next.

In the next window (Source Git Repository) you should put the git clone URL in the text box labelled URI. If you have a Jalview developer account (with a username and password for the Jalview git repository) then you should enter https://source.jalview.org/git/jalview.git. If you do not have a Jalview developer account then you should enter http://source.jalview.org/git/jalview.git. You will not be able to push any of your changes back to the Jalview git repository. However you can still pull all branches of the Jalview source code to your computer and develop the code there.

You can sign up for a Jalview developer account at https://source.jalview.org/crucible/

If you have a Jalview developer account, enter the username and password and decide if you want to use Eclipse’s secure storage. If you don’t have an account you can leave the Authentication section blank.

Click on the Next button.

The next window (Branch Selection) gives a list of the many Jalview branches, which by default will be all checked. You probably only want to download one branch (you can always download others at a later time). This is likely to be the develop branch so you can click on the Deselect All button, find the develop branch (the filter text helps), select that, and then click on the Next button.

Choose a directory to your copy of the git repo in, and leave the other options as they are and click on the Next button. The next stage may take a minute or two as it checks out the selected branch(es) from the Jalview git repository.

When it has finished it is important to select Import as general project and then click on Next.

Ideally there would be an Import as gradle project here but there isn’t – we’ll sort that out later.

Click on the Next button.

You can change the project name here. By default it will show as jalview which is fine unless you have another instance of the a Jalview project also called jalview, in which case you could change this project’s name now to avoid a conflict within Eclipse.

Click on Finish!

However, we haven’t finished…

You should now see, and be able to expand, the jalview project in the Project Explorer. We need to tell eclipse that this is a Gradle project, which will then allow the Eclipse Buildship plugin to automatically configure almost everything else!

Right click on the project name (jalview) in the Project Explorer and find Configure towards the bottom of this long context menu, then choose Add Gradle Nature.

The project should now reconfigure itself using the build.gradle file to dynamically set various aspects of the project including classpath.

Additional views

Some views that are automatically added when Importing a Gradle Project are not added when simply Adding a Gradle Nature, but we can add these manually by clicking on Window->Show View->Console and Window->Show View->Other… Filter with the word “gradle” and choose both Gradle Executions and Gradle Tasks and then click on the Open button.

Okay, ready to code! Use of Eclipse is beyond the scope of this document, but you can find more information about developing jalview and our developer workflow in the google doc https://docs.google.com/document/d/1lZo_pZRkazDBJGNachXr6qCVlw8ByuMYG6e9SZlPUlQ/edit?usp=sharing

Jalview Development Team