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Jar with dependencies not included in zip file with maven assembly plugin

I am using maven assembly plugin to generate a zip file containing my jar including all dependencies, however the jar included does not contain all the jars when i use this command:
jar tf jar-included-in-the-zip.jar
Here is my configuration:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<finalName>my-jar</finalName>
</configuration>
<executions>
<execution>
<id>assembly-id</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<classifier></classifier>
<descriptors>
<descriptor>assembly.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
and here is my assembly:
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.3"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.3 http://maven.apache.org/xsd/assembly-1.1.3.xsd">
<id>xxx</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<fileSets>
<fileSet>
<directory>${my-jar.target.dir}</directory>
<outputDirectory>${my-jar.ouput.dar.dir}/${version}</outputDirectory>
<includes>
<include>**/*.jar</include>
</includes>
</fileSet>
</fileSets>
In target i get a jar containing all dependencies, and a zip containing a jar that does not include the dependencies. How can i get to include my jar with dependencies into the zip file.

Try with this kind of configuration. I don't think whether you need assembly.xml. You can have all your dependencies as a part of your jar file itself if they are available on classpath. Is there any specific need for zip file in your case?
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<finalName>${project.artifactId}</finalName>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>{your.package.name.MainClass}</mainClass>
</manifest>
</archive>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

Try to replace
<include>**/*.jar</include>
by
<include>*:jar:*</include>
in your assembly.xml

Building jar with dependency and bundling it in tar.gz using maven assembly

I want to build an executable jar and need to bundle it with some scripts file in tar.gz file for that I'm using maven assembly which looks like below
pom.xml
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<finalName>${final.jar.name}</finalName>
<appendAssemblyId>false</appendAssemblyId>
<archive>
<manifest>
<mainClass>path.to.main.class</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<descriptors>${project.basedir}/assembly.xml</descriptors>
</configuration>
<executions>
<execution>
<id>trigger-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
assembly.xml
<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.3"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.3 http://maven.apache.org/xsd/assembly-1.1.3.xsd">
<id>connection-ai-jira-integration-assembly</id>
<includeBaseDirectory>false</includeBaseDirectory>
<formats>
<format>tar.gz</format>
</formats>
<files>
<file>
<source>${project.build.directory}/${project.build.finalName}.jar</source>
<outputDirectory>/lib/</outputDirectory>
<filtered>true</filtered>
</file>
</files>
<fileSets>
<fileSet>
<directory>${basedir}/script/</directory>
<includes>
<include>*.*</include>
</includes>
<outputDirectory>/script/</outputDirectory>
<filtered>true</filtered>
</fileSet>
</fileSets>
But when i execute build then the jar is getting copied to tar.gz file but of different size and corrupted. Can someone point where I'm mistaking, thanks in advance.

OpenIMAJ: Maven MojoExecutionException [duplicate]

Following this Guide I ran the command
mvn assembly:assembly
and got the Build Failure of
Error reading assemblies: No assembly descriptors found.
I've looked at numerous questions on this, but to no avail.
From this post, I created a .xml with this inside:
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>jar-with-dependencies</id>
<formats>
<format>jar</format>
</formats>
<dependencySets>
<dependencySet>
<scope>runtime</scope>
<unpack>true</unpack>
<unpackOptions>
<excludes>
<exclude>**/LICENSE*</exclude>
<exclude>**/README*</exclude>
</excludes>
</unpackOptions>
</dependencySet>
</dependencySets>
<fileSets>
<fileSet>
<directory>${project.build.outputDirectory}</directory>
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
</fileSet>
<fileSet>
<directory>src/main/resources/META-INF/services</directory>
<outputDirectory>META-INF/services</outputDirectory>
</fileSet>
</fileSets>
</assembly>
and included this in the pom.xml:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
<descriptors>
<descriptor>jar-with-dependencies.xml</descriptor>
</descriptors>
</configuration>
</plugin>
but still no luck.
I'm pretty new to this as you can probably tell, how can I get this running?
~~EDIT~~
In the pom.xml I changed
<descriptor>jar-with-dependencies.xml</descriptor>
To
<descriptor>src/main/assembly/jar-with-dependencies.xml</descriptor>
~~EDIT 2~~
pom.xml now contains this:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptors>
<descriptor>src/main/assembly/jar-with-dependencies.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
~~EDIT 3~~
This pom.xml now works for me:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
<descriptors>
<descriptor>src/main/assembly/jar-with-dependencies.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

For this to work, you need to create the file jar-with-dependencies.xml in src/main/assembly/ and this XML:
<descriptors>
<descriptor>src/main/assembly/jar-with-dependencies.xml</descriptor>
</descriptors>
i.e. you need to specify the path to the file and the convention is to put the files into src/main/assembly/.
To use the ones provided by Maven, you need to use the descriptorRef element instead (wrapped in a descriptorRefs).
Also don't put the descriptor inside of the execution element or mvn assembly:assembly can't find it anymore (since you specifically moved it to the mvn package target).
[EDIT] I followed the tutorial myself and there is an important point which you might have missed: You need to select the correct archetype. In my case, that was 5 but the order can change. So read the whole list and look for the string openimaj-quickstart-archetype or things will break.

Is the content of the Maven Assesmnly plugin's jar-with-dependencies descriptorRef documented as an example assembly descriptor file anywhere?

The following see How can I create an executable jar with dependencies using Maven? shows how to create an executable jar with the Maven plugin.
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
However I wish to exclude some of the dependencies which are in my POM. All I want to do is to add
<dependencySets>
<dependencySet>
<useStrictFiltering>true</useStrictFiltering>
<scope>compile</scope>
<excludes>
<exclude>com.excluded:artifact</exclude>
</excludes>
</dependencySet>
</dependencySets>
to the above but I cannot , because I need to add that in a separate assembly descriptor. What I want to do is exactly the same as jar-with-dependencies but with the exclusion. Is there somewhere where an equivalent assembly descriptor file is described so I can edit it? Is there any way to 'inherit' jar-with-dependencies and add my exclusions?

I think that you can use scope "compile" :
<dependency>
<groupId>com.xxxx</groupId>
<artifactId>xxxxxx</artifactId>
<version>3.x</version>
<scope>compile</scope>
</dependency>

See The Maven Documentation on pre defined descriptors for the equivalent of jar-with-depedencies.
So I can change the POM I am using to build 'super jar' as follows;
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>my.Main</mainClass>
</manifest>
</archive>
<descriptors>
<descriptor>src/main/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
<!-- Uncomment this for automatic creation of the Complete jar
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
-->
</plugin>
And in the directory src/main/assembly/assembly.xml I can put the following which is essentially the same as the jar-with-dependencies descriptor with my exclusions;
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<!-- TODO: a jarjar format would be better -->
<id>jar-with-dependencies</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<outputDirectory>/</outputDirectory>
<useProjectArtifact>true</useProjectArtifact>
<unpack>true</unpack>
<scope>runtime</scope>
<excludes>
<exclude>com.local.depedency:artifact_id</exclude>
<exclude>transitive.depedency.so.way.down:artifact_id</exclude>
</excludes>
</dependencySet>
</dependencySets>
</assembly>

Maven plugin to create executable jar with dependencies not unpacked (jar with jars)

I read a lot of solutions to build executable jar with dependencies (maven shade plugin, maven dependency plugin, maven assembly plugin) and all of this plugins unpack dependency jars and repack them in executable jar. The only plugin that pack dependency jars unpacked in executable jar is one jar plugin but this plugin add its runner code in executable jar.
Is there any solution to create jar like this:
├─executable.jar
├──lib/
├───dependency1.jar
├───dependency2.jar
.
.
.
and that solution to work.

The most common way is to use assembly plugin which will allow you to configure packaging in a way you need
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.somewhere.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
Also you can specify assembly descriptor for configuration
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/main/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
And assembly.xml itself
<assembly>
<id>assembly</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<fileSets>
<fileSet>
<directory>${project.build.outputDirectory}</directory>
<outputDirectory>/</outputDirectory>
</fileSet>
</fileSets>
</assembly>
Assembly descriptor can also contain dependency section:
<!-- lib -->
<dependencySets>
<dependencySet>
<outputDirectory>lib</outputDirectory>
</dependencySet>
</dependencySets>
As far as I understand you're looking for the last one. As it just includes jar files into the assembly without any modifications. So the final solution will look like:
<assembly>
<id>assembly</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<!-- lib -->
<dependencySets>
<dependencySet>
<outputDirectory>lib</outputDirectory>
</dependencySet>
</dependencySets>
</assembly>
and pom part:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/main/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

<plugins>
<plugin>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<additionalProjectnatures>
<projectnature>org.springframework.ide.eclipse.core.springnature</projectnature>
</additionalProjectnatures>
<additionalBuildcommands>
<buildcommand>org.springframework.ide.eclipse.core.springbuilder</buildcommand>
</additionalBuildcommands>
<downloadSources>true</downloadSources>
<downloadJavadocs>true</downloadJavadocs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5.1</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
<compilerArgument>-Xlint:all</compilerArgument>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<configuration>
<mainClass>org.test.int1.Main</mainClass>
</configuration>
</plugin>
</plugins>