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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
83 stars 21 forks source link

Error when packaging uber jar #583

Closed e5c closed 7 years ago

e5c commented 7 years ago

Running mvn package -Puber -DskipTests on master at head yields,

$ mvn package -Puber -DskipTests

...

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:2.1:shade (deps) on project guacamole: Error creating shaded jar: Error in ASM processing class htsjdk/samtools/BAMIndexer.class: 2560 -> [Help 1]

Full stack trace: gist

Maven version info:

$ mvn -V

Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-10T11:41:47-05:00)
Maven home: /hpc/users/change07/apache-maven-3.3.9
Java version: 1.8.0_91, vendor: Oracle Corporation
Java home: /demeter/users/change07/bin/jdk1.8.0_91/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.10.0-327.4.5.el7.x86_64", arch: "amd64", family: "unix"

However mvn package -Pguac,deps -DskipTests works.