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Problem building gatk-protected from github

I tried just now to checkout and build gatk-protected from the github repo. However, I ran afoul of the following problem (see below for error message). I'm guessing that it's originating from some unresolved dependency in the pom file. However, my knowledge of maven is somewhat sketchy.

I check it out from github git clone https://github.com/broadgsa/gatk-protected.git and build it with the mvn package.

[email protected]:~/workspace/gatk-protected$ mvn package
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] GATK Root
[INFO] GATK Aggregator
[INFO] GATK GSALib
[INFO] GATK Utils
[INFO] GATK Engine
[INFO] GATK Tools Public
[INFO] External Example
[INFO] GATK Queue
[INFO] GATK Queue Extensions Generator
[INFO] GATK Queue Extensions Public
[INFO] GATK Aggregator Public
[INFO] GATK Tools Protected
[INFO] GATK Package Distribution
[INFO] GATK Queue Extensions Distribution
[INFO] GATK Queue Package Distribution
[INFO] GATK Aggregator Protected
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK Root 3.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-root ---
[INFO] [git, describe, --long]
[INFO] Setting Git Describe: git-3.2-0-g799071b
[INFO] 
[INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-root ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK Aggregator 3.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gatk-aggregator ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gatk-aggregator ---
[INFO] 
[INFO] --- exec-maven-plugin:1.2.1:exec (delete-mavens-links) @ gatk-aggregator ---
rm: missing operand
Try 'rm --help' for more information.
rm: missing operand
Try 'rm --help' for more information.
[INFO] 
[INFO] --- maven-junction-plugin:1.0.3:link (link-public-testdata) @ gatk-aggregator ---
[INFO] 
[INFO] --- maven-junction-plugin:1.0.3:link (link-public-qscript) @ gatk-aggregator ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK GSALib 3.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- gitdescribe-maven-plugin:2.0:gitdescribe (gitdescribe-initialize) @ gsalib ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.8:regex-property (fix-version-initialize) @ gsalib ---
[INFO] 
[INFO] --- maven-assembly-plugin:2.4:single (gsalib-assembly) @ gsalib ---
[INFO] Reading assembly descriptor: src/assembly/gsalib.xml
[INFO] Building tar: /home/dahljo/workspace/gatk-protected/public/gsalib/target/gsalib-3.2-SNAPSHOT.tar.gz
[INFO] 
[INFO] --- maven-junction-plugin:1.0.3:link (link-public-testdata) @ gsalib ---
[INFO] 
[INFO] --- maven-junction-plugin:1.0.3:link (link-public-qscript) @ gsalib ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK Utils 3.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: file:/home/dahljo/workspace/gatk-protected/public/gatk-utils/../../public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
Exception in thread "pool-1-thread-1" ---------------------------------------------------
constituent[0]: file:/usr/share/maven/lib/sisu-inject-bean.jar
java.lang.NoClassDefFoundError: org/apache/commons/lang/StringUtilsconstituent[1]: file:/usr/share/maven/lib/commons-cli.jar

constituent[2]: file:/usr/share/maven/lib/maven-compat-3.x.jar
    at org.apache.maven.wagon.providers.file.FileWagon.resolveDestinationPath(FileWagon.java:206)
constituent[3]: file:/usr/share/maven/lib/aether-util.jar
    at org.apache.maven.wagon.providers.file.FileWagon.resourceExists(FileWagon.java:265)constituent[4]: file:/usr/share/maven/lib/maven-artifact-3.x.jar

    at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:577)constituent[5]: file:/usr/share/maven/lib/wagon-http-shaded.jar

    at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:60)constituent[6]: file:/usr/share/maven/lib/maven-repository-metadata-3.x.jar

    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)constituent[7]: file:/usr/share/maven/lib/commons-httpclient.jar

constituent[8]: file:/usr/share/maven/lib/plexus-utils.jar
constituent[9]: file:/usr/share/maven/lib/aether-connector-wagon.jarCaused by: java.lang.ClassNotFoundException: org.apache.commons.lang.StringUtils

constituent[10]: file:/usr/share/maven/lib/plexus-interpolation.jar at org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)

constituent[11]: file:/usr/share/maven/lib/aether-impl.jar
    at org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:259)
constituent[12]: file:/usr/share/maven/lib/maven-settings-3.x.jar
    at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:235)constituent[13]: file:/usr/share/maven/lib/sisu-guice.jar

    at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:227)constituent[14]: file:/usr/share/maven/lib/guava.jar

    ... 7 moreconstituent[15]: file:/usr/share/maven/lib/commons-codec.jar

constituent[16]: file:/usr/share/maven/lib/wagon-provider-api.jar
constituent[17]: file:/usr/share/maven/lib/plexus-component-annotations.jar
constituent[18]: file:/usr/share/maven/lib/maven-plugin-api-3.x.jar
constituent[19]: file:/usr/share/maven/lib/maven-settings-builder-3.x.jar
constituent[20]: file:/usr/share/maven/lib/maven-model-builder-3.x.jar
constituent[21]: file:/usr/share/maven/lib/plexus-cipher.jar
constituent[22]: file:/usr/share/maven/lib/maven-model-3.x.jar
constituent[23]: file:/usr/share/maven/lib/commons-logging.jar
constituent[24]: file:/usr/share/maven/lib/sisu-inject-plexus.jar
constituent[25]: file:/usr/share/maven/lib/maven-core-3.x.jar
constituent[26]: file:/usr/share/maven/lib/aether-api.jar
constituent[27]: file:/usr/share/maven/lib/maven-aether-provider-3.x.jar
constituent[28]: file:/usr/share/maven/lib/maven-embedder-3.x.jar
constituent[29]: file:/usr/share/maven/lib/aether-spi.jar
constituent[30]: file:/usr/share/maven/lib/plexus-sec-dispatcher.jar
constituent[31]: file:/usr/share/maven/lib/wagon-file.jar
---------------------------------------------------
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/lang/StringUtils
    at org.apache.maven.wagon.providers.file.FileWagon.resolveDestinationPath(FileWagon.java:206)
    at org.apache.maven.wagon.providers.file.FileWagon.resourceExists(FileWagon.java:265)
    at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:577)
    at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:60)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.lang.StringUtils
    at org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
    at org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:259)
    at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:235)
    at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:227)
    ... 7 more

This is my environment info on maven:

[email protected]:~/workspace/gatk-protected$ mvn -version
Apache Maven 3.0.5
Maven home: /usr/share/maven
Java version: 1.7.0_45, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-oracle/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.13.0-30-generic", arch: "amd64", family: "unix"

Has anybody else seen this?

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