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larryns / MitoScape

A big-data, machine-learning workflow for aligning mtDNA from NGS data.
Apache License 2.0
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Deduplication Errors #2

Closed aledavini7 closed 2 years ago

aledavini7 commented 2 years ago

Hello, I am trying to use MitoScape following the instructions available on github. I have cloned the repository and I have typed the command "sbt assembly" to generate the fat jar. I am working with Java=8 as suggested in the buld.sbt file.

When I run the command I obtain a long list of errors saying: "deduplicate: different file contents found in the following:"

I copy below few lines as example:

[error] deduplicate: different file contents found in the following: [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.3-1/jaxb-impl-2.2.3-1.jar:com/sun/xml/bind/v2/runtime/reflect/TransducedAccessor.class [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-runtime/2.3.2/jaxb-runtime-2.3.2.jar:com/sun/xml/bind/v2/runtime/reflect/TransducedAccessor.class [error] deduplicate: different file contents found in the following: [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.3-1/jaxb-impl-2.2.3-1.jar:com/sun/xml/bind/v2/runtime/reflect/opt/AccessorInjector.class [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-runtime/2.3.2/jaxb-runtime-2.3.2.jar:com/sun/xml/bind/v2/runtime/reflect/opt/AccessorInjector.class ... ... [error] deduplicate: different file contents found in the following: [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/com/sun/jersey/jersey-core/1.9/jersey-core-1.9.jar:javax/ws/rs/core/SecurityContext.class [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/jakarta/ws/rs/jakarta.ws.rs-api/2.1.6/jakarta.ws.rs-api-2.1.6.jar:javax/ws/rs/core/SecurityContext.class [error] deduplicate: different file contents found in the following: [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/com/sun/jersey/jersey-core/1.9/jersey-core-1.9.jar:javax/ws/rs/core/StreamingOutput.class [error] /hpcnfs/home/ieo5898/.cache/coursier/v1/https/repo1.maven.org/maven2/jakarta/ws/rs/jakarta.ws.rs-api/2.1.6/jakarta.ws.rs-api-2.1.6.jar:javax/ws/rs/core/StreamingOutput.class ... ...

Is there perhaps some adjustment I have to make in the build.sbt "assemblyMergeStrategy"?

Thank you a lot! Alessandro

larryns commented 2 years ago

Hi Alessandro,

Yes, the fat jar is a pain to create. There have been some upgrades to sbt and associate plugins and unfortunately with those, the fat jar build won't work. I have updated the config files, so try cloning the git again and trying the assembly again. It should work now.

In the future I won't be supporting the fat jar, just the Docker image (maybe Singularity). So keep that in mind.

Let me know if the new changes work for you.

Thanks, Larry.

aledavini7 commented 2 years ago

Thank you very much for the quick reply. I have cloned the git, tried the assembly again and now everything work!

Thank you! Alessandro