groovy script library requirements

[janders3-nmdp]

It's still pulling libraries out of Caleb's Homedir, and the /tmp/hla-a.txt file.

We should add hla-a.txt into tutorial, and ensure the required libraries are in a system directory, so I can mirror them into an AMI.

The Tutorial documentation should then also be updated.

[ghost]

Alternatively, we could build the groovy script using gradle, ant, ivy, or maven, and build an executable using a groovy build plugin equivalent to the maven appassembler plugin.

[janders3-nmdp]

I rather like that approach -- would it allow us to include the various hla-*.txt files directly into it, and just select them with something like a command-line flag?

[ckennedy-nmdp]

We could do that, although we're almost done porting to Java anyway. Probably best to wait.

C

[ckennedy-nmdp]

I think we should have a post-hackathon release relatively soon, perhaps coinciding with publication of HML 1.0.

[ghost]

@ckennedy-nmdp ping, we desperately need this

[ckennedy-nmdp]

• htsjdk-1.118.jar
• ngs-feature-x.x-SNAPSHOT.jar
• biojava.jar (LEGACY)
• bzip2.jar
• guava-17.0.jar

[andersje]

Is this just the list of required libraries I need to add into the repo? Or is there also an associated PR somewhere which incorporates these?

[ghost]

splice-bam.groovy may be replaced in the near future by the port to java, ngs-filter-consensus

https://github.com/nmdp-bioinformatics/ngs/pull/59

[ghost]

@ckennedy-nmdp can splice-bam.groovy be removed from the git repo and this issue be closed at this point?

[ckennedy-nmdp]

Yes, the Java port has been fully validated. Please deprecate splice-bam.groovy and remove from the repository.

[ghost]

Cloing this as WontFix, created new issue #89