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heuermh broadinstitute fnothaft tdanford massie adomore b3ds-d01

bdg-services's Issues

Move to ADAM 0.14.1-SNAPSHOT

Attempting to update dependencies Scala to version 2.10.4, Spark to version 1.1, and ADAM to version 0.14.1-SNAPSHOT fails to compile

$ mvn clean install
...
[INFO] Compiling 6 Scala sources to working/bdg-services/bdgs-core/target/scala-2.10.4/classes...
[ERROR] working/bdg-services/bdgs-core/src/main/scala/org/bdgenomics/services/ServiceContext.scala:39: value createSparkContext is not a member of object org.bdgenomics.adam.rdd.ADAMContext
[ERROR]     ADAMContext.createSparkContext(
[ERROR]                 ^
[ERROR] one error found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] BDG Services: Service setup and management for BDG Projects SUCCESS [  4.238 s]
[INFO] BDGS: Core ......................................... FAILURE [ 12.321 s]

Don't hard code all the JARs to be packaged

In #2, we added spark context creation code, and right now have hard coded all of the JARs to add. Some of the JARs should always be hardcoded, but we shouldn't hard code all of them.

Maven plugin build warnings 

$ mvn clean install
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-reads:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ org.bdgenomics.services:bdgs-reads:[unknown-version], /Users/xxx/working/bdg-services/bdgs-reads/pom.xml, line 115, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ org.bdgenomics.services:bdgs-reads:[unknown-version], /Users/xxx/working/bdg-services/bdgs-reads/pom.xml, line 169, column 21
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-cli:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ org.bdgenomics.services:bdgs-cli:[unknown-version], /Users/xxx/working/bdg-services/bdgs-cli/pom.xml, line 115, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ org.bdgenomics.services:bdgs-cli:[unknown-version], /Users/xxx/working/bdg-services/bdgs-cli/pom.xml, line 166, column 21
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-service-manager:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ org.bdgenomics.services:bdgs-service-manager:[unknown-version], /Users/xxx/working/bdg-services/bdgs-service-manager/pom.xml, line 128, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ org.bdgenomics.services:bdgs-service-manager:[unknown-version], /Users/xxx/working/bdg-services/bdgs-service-manager/pom.xml, line 181, column 21
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]

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