Installing VDJdb server

First make sure that you have installed Java Runtime Environment (JRE) v1.8 by running java -version. Any recent Linux distribution will provide it via its package manager. If not, or if your system is running MacOSX or Windows, download the JRE, for example, from Oracle.

Installing binaries

The most straightforward way to install VDJdb as a local server is to download the latest release package.

After downloading unzip the package wherever you want, but please avoid long paths and spaces (Windows version is especially sensitive to it).

You can find the server executable in bin/ directory. To set up the server:

• Run vdjdb-web.bat file (Windows)
• Run ./vdjdb-web in your console (Linux/Mac OS)

Wait until the server is started, and go to localhost:9000 URL in your browser to open VDJdb.

To stop application just press Ctrl-C at any time in console.

Note

Note that an exception will be thrown in case the 9000 port is busy: org.jboss.netty.channel.ChannelException: Failed to bind to: /0.0.0.0:9000. In order to fix it, either close the application that is using this port (in UNIX the lsof -i:9000 will give the processes that are using the port) or pass the -Dhttp.port=XXXX (where XXXX is new port id) argument to vdjdb-web shell script (UNIX) / vdjdb-web.bat (Windows)

Compiling from sources

Back-end dependencies

• VDJtools
• VDJmatch
• Scala Build Tools
• Java 1.8

Please check that the versions of VDJtools and VDJmatch are matched to that in build.sbt file coming with VDJdb-server.

Front-end dependencies

• Node.js 11 and NPM 6
• Yarn 1.22

Compiling

VDJdb could be compiled from source using Scala Build Tools (SBT). Compilation should be performed under JRE v1.8 by running the following commands:

$ git clone https://github.com/antigenomics/vdjdb-web.git
$ cd vdjdb-web/
$ sbt
[VDJdb-server] $ frontendInstallDependencies
[VDJdb-server] $ build

Binaries could then be found under the target/universal/vdjdb-server-X.Y.Z.zip package.

SBT console commands

SBT console supports some utility functions which can be executed in the following way.

$ sbt
$ [VDJdb-server] $ command1
$ [VDJdb-server] $ command2

Available commands:

Command	Description
build	Build VDJdb application
backendBuild	Build VDJdb backend only
backendTest	Test VDJdb backend
frontendBuild	Build VDJdb frontend bundle only
frontendCleanDependencies	Clean frontend dependencies
frontendCleanBuild	Clean frontend build
frontendInstallDependencies	Install frontend dependencies
frontendOutdated	Check frontend dependencies updates

Warning

Note that after frontendCleanDependencies command will be executed other commands with frontend prefix (excluding frontendInstallDependencies) will be unavailable.