Eclipse is not using gradle dependencies jar during run or debug - eclipse

I am trying to do basic hibernate task using Gradle project.
Dependency jars are download by Gradle and placed in Project and External Dependencies library.
I don't get any compile time error. But when I try to run or debug the main class in Eclipse, I am getting class not found NoClassDefFoundError.
Exception in thread "main" java.lang.NoClassDefFoundError: org/hibernate/cfg/Configuration
When I checked the build path, I could see the dependency library is configured with required jars but still eclipse is not using it.
But when I add the jar manually in the build path, I am not getting this exception.
Build.gradle File
plugins {
// Apply the java-library plugin to add support for Java Library
id 'java-library'
}
apply plugin: "eclipse"
dependencies {
// This dependency is exported to consumers, that is to say found on their compile classpath.
api 'org.apache.commons:commons-math3:3.6.1'
// This dependency is used internally, and not exposed to consumers on their own compile classpath.
implementation 'com.google.guava:guava:23.0'
// Use JUnit test framework
testImplementation 'junit:junit:4.12'
// https://mvnrepository.com/artifact/org.hibernate/hibernate-core
compile group: 'org.hibernate', name: 'hibernate-core', version: '5.3.6.Final'
// https://mvnrepository.com/artifact/com.oracle.jdbc/ojdbc6
runtime group: 'com.oracle.jdbc', name: 'ojdbc6', version: '11.1.0.6.0'
// https://mvnrepository.com/artifact/com.oracle/ojdbc6
runtime group: 'com.oracle', name: 'ojdbc6', version: '11.2.0.4.0-atlassian-hosted'
}
// In this section you declare where to find the dependencies of your project
repositories {
// Use jcenter for resolving your dependencies.
// You can declare any Maven/Ivy/file repository here.
jcenter()
mavenCentral()
}
Thanks in advance!!!

I think you should update the classpath with the latest changes in the build file. Eclipse does not do that automatically in all versions.
Go to package explorer, right-click the build.gradle file, then from the context menu select gradle->refresh gradle project.
You can also enable auto sync from the preferences menus, go to gradle, and check the "Automatic Project Synchronization" checkbox.

Remove/comment this dependency and try.
runtime group: 'com.oracle.jdbc', name: 'ojdbc6', version: '11.1.0.6.0'
My Build.gradle:
plugins {
// Apply the java-library plugin to add support for Java Library
id 'java-library'
}
dependencies {
// This dependency is exported to consumers, that is to say found on their compile classpath.
api 'org.apache.commons:commons-math3:3.6.1'
// This dependency is used internally, and not exposed to consumers on their own compile classpath.
implementation 'com.google.guava:guava:23.0'
// Use JUnit test framework
testImplementation 'junit:junit:4.12'
// https://mvnrepository.com/artifact/org.hibernate/hibernate-core
compile group: 'org.hibernate', name: 'hibernate-core', version: '5.3.6.Final'
// https://mvnrepository.com/artifact/com.oracle.jdbc/ojdbc6
// runtime group: 'com.oracle.jdbc', name: 'ojdbc6', version: '11.1.0.6.0'
// https://mvnrepository.com/artifact/com.oracle/ojdbc6
runtime group: 'com.oracle', name: 'ojdbc6', version: '11.2.0.4.0-atlassian-hosted'
}
// In this section you declare where to find the dependencies of your project
repositories {
// Use jcenter for resolving your dependencies.
// You can declare any Maven/Ivy/file repository here.
jcenter()
}

With the eclipse plugin, there are different build tasks being added:
./gradlew cleanEclipse eclipse

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Publish your plugin jar to a repository, along with the necessary metadata (which Gradle will do for you) and bring it in as an external module dependency
Explicitly declare the plugin's transitive dependencies using a client module dependency.
Use something like the Gradle fatjar or shadow plugins to bundle dependencies within your jar.