To Build

Ensure that you have at least Java 21

BioUML uses a dual build system (Maven + Ant). Both must compile successfully.

Manually install JARs missing in Maven Central

./install_all_old_jars.sh 

Maven (modern, multi-module):

mvn package -DskipTests

Ant (legacy):

cd src && ant compile

Verify both after any change:

mvn package -DskipTests && cd src && ant compile

To Run

First, start mysql server. The command below is for docker but you can easiliy adopt it to your situation

docker run --name mysql-biouml2 \
   -p 3306:3306 \
   -v ./dumps/bioumlsupport2.dump.sql:/docker-entrypoint-initdb.d/bioumlsupport2.dump.sql \
   -e MYSQL_ROOT_PASSWORD=biouml \
   -e MYSQL_DATABASE=bioumlsupport2 \
   -e MYSQL_USER=bioumlsupport2 \
   -e MYSQL_PASSWORD=bioumlsupport2 \
   -d mysql:5

Alternatively, you can launch mysql server via docker-compose

Then launch BioUML Web edition.

mvn -pl tomcat-embedded exec:java

For Java versions newer than 11 you can use experimental forked launch mode

mvn -pl tomcat-embedded exec:exec@run-forked

Use your browser to open it at http://localhost:8080/bioumlweb/

To Run tests

On Linux install required packages

sudo apt install r-base r-base-dev

Ensure that you have at least Java 21

mvn -pl src test 

or simply

mvn test