utils-java

This project's goal is to reduce duplicate code across different Google Genomics Java integrations.

If you have duplicate code appearing in your projects, or see useful functions in the other googlegenomics Java repositories that you want to depend on, please contribute!

##Depending on this project

Note: you can find the latest available version of this project in Maven's central repository.

Maven

Add the following to your pom.xml file:

<project>
  <dependencies>
    <dependency>
      <groupId>com.google.cloud.genomics</groupId>
      <artifactId>google-genomics-utils</artifactId>
      <version>v1beta2-0.1</version>
    </dependency>
  </dependencies>
</project>

Gradle

Add the following to your build.gradle file:

repositories {
    mavenCentral()
}

dependencies {
    compile 'com.google.cloud.genomics:google-genomics-utils:v1beta2-0.1'
}

##The code

• GenomicsFactory.java makes it easier to construct an authenticated Genomics service
• Paginator.java lazily paginates through readsets, reads, variants and callsets

##Releasing new versions

This section contains details on getting a new release into Maven central and can be safely ignored by most people. If you need a new release of this code, go ahead and just file an issue.

###Prereqs

• File a ticket to get access to the Sonatype com.google.cloud.genomics group
• Setup gpg (Don't forget to publish a public key)
• Setup GitHub SSH keys (make sure ssh -T [email protected] works)
• Create a ~/.m2/settings.xml file which has the following:

<settings>
  <servers>
    <server>
      <id>ossrh</id>
      <username>sonatype-username</username>
      <password>sonatype-password</password>
    </server>
  </servers>
</settings> 

###Making a new release

1. Use Maven to tag the code, up the pom version and release into the Sonatype staging area.

mvn release:prepare
mvn release:perform

2. Find the repository at https://oss.sonatype.org/#stagingRepositories and close it.
3. If closing succeeds, then release it. See the detailed instructions for more info.
4. As long as there aren't any errors - that's it! The new version will be synced to Maven central.