Gradle fatJar/uberJar causing Could not find or load main class

Question

I'm having an issue where gradle fatJar/uberJar is causing the following exception when trying to run the jar:

Error: Could not find or load main class com.domhauton.membrane.Main

The simple jar task without

from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
with jar

works with no issues (up to the point where it starts needing dependencies).

I presume this is to do with one of my dependencies changing the classpath, but I'm not sure why that would be happening.

Relevant part of build.gradle

project.version = '1.0.0-alpha.2'
project.group = 'com.domhauton.membrane'

jar {
    baseName = 'membrane-daemon-simple'
    version = project.version
    manifest {
        attributes 'Implementation-Title': 'Membrane Daemon',
                'Implementation-Version': project.version,
                'Main-Class': project.group + '.Main'
    }
}

//create a single Jar with all dependencies
task fatJar(type: Jar) {
    manifest {
        attributes 'Implementation-Title': 'Membrane Daemon',
                'Implementation-Version': project.version,
                'Main-Class': project.group + '.Main'
    }
    baseName = 'membrane-daemon'
    version = project.version
    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
    with jar
}

Gradle build file is here (with the remainder of code):

https://github.com/domhauton/membraned/blob/master/build.gradle

The META-INF folder is very full of files from the other dependencies so I'm not sure where to start looking for conflicts.

Answer 1

Took another run at the problem using shadowjar and it worked flawlessly.

Relevant code:

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath group: 'com.github.jengelman.gradle.plugins', name: 'shadow', version: '1.2.4'
    }
}

apply plugin: 'com.github.johnrengelman.shadow'

project.version = '1.0.0-alpha.2'
project.group = 'com.domhauton.membrane'

jar {
    baseName = 'membrane-daemon'
    version = project.version
    manifest {
        attributes 'Implementation-Title': 'Membrane Daemon',
                'Implementation-Version': project.version,
                'Main-Class': project.group + '.Main'
    }
}

Can be seen in context here: https://github.com/domhauton/membraned/blob/4d28ea451acc5bf52724a0cc5c94823659236287/build.gradle