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created by LeeTL1220
on 2016-05-16
use .hdfview-2.9 use Java-1.8 use .r-3.1.3-gatk-only
If these don’t work, move to a VM where the dotkits are not broken.
From yrx on 2016-05-27
In build.grade script: compile ‘com.github.lindenb:jbwa:bd72b489f9697a857671533c86ad5906967f8672-20160521.042635-1’
//needed for DataflowAssert testCompile ‘org.hamcrest:hamcrest-all:1.3‘ testCompile ‘junit:junit:4.12‘ testCompile “org.mockito:mockito-core:1.10.19“ }
def findJarByName(Configuration config, String name) { config.filter { it.name.startsWith(name)}.singleFile
}
While running ./gradlew installAll, error message as following:
FAILURE: Build failed with an exception.
- What went wrong:
- Could not resolve all dependencies for configuration ‘:sparkConfiguration’.
- > Could not resolve com.github.lindenb:jbwa:bd72b489f9697a857671533c86ad5906967f8672-20160521.042635-1. Required by: org.broadinstitute:gatk:4.alpha.1-92-g543ceb7-SNAPSHOT > Could not resolve com.github.lindenb:jbwa:bd72b489f9697a857671533c86ad5906967f8672-20160521.042635-1. > Could not get resource ‘https://artifactory.broadinstitute.org/artifactory/libs-snapshot/com/github/lindenb/jbwa/bd72b489f9697a857671533c86ad5906967f8672-SNAPSHOT/jbwa-bd72b489f9697a857671533c86ad5906967f8672-20160521.042635-1.pom’. > Could not GET ‘https://artifactory.broadinstitute.org/artifactory/libs-snapshot/com/github/lindenb/jbwa/bd72b489f9697a857671533c86ad5906967f8672-SNAPSHOT/jbwa-bd72b489f9697a857671533c86ad5906967f8672-20160521.042635-1.pom’. > Received fatal alert: handshake_failure
How to fix?
From LeeTL1220 on 2016-05-31
@yrx For some reason, my initial post did not work… Anyway: Try ``./gradlew clean shadowJar``