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build.sbt
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build.sbt
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import java.text.SimpleDateFormat
import java.util.Date
import com.typesafe.sbt.SbtGit.GitCommand
import sbt.Keys._
import sbt._
import sbtassembly.AssemblyKeys.assembly
import scoverage.ScoverageKeys._
import scala.sys.process.Process
////////////////////////////////////////////////////////////////////////////////////////////////
// Multi-project build file for the following projects:
// - commons: utility code and base classes used across projects
// - calitas: code for the CALITAS aligner
////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////
// Common settings for all projects
////////////////////////////////////////////////////////////////////////////////////////////////
val htmlReportsDirectory: String = "target/test-reports"
lazy val htsjdkAndPicardExcludes = Seq(
ExclusionRule(organization="org.apache.ant"),
ExclusionRule(organization="gov.nih.nlm.ncbi"),
ExclusionRule(organization="org.testng"),
ExclusionRule(organization="com.google.cloud.genomics")
)
lazy val ToolkitVersion = {
val date = new SimpleDateFormat("yyyyMMdd").format(new Date())
val hash = Process("git rev-parse --short HEAD").lineStream.head
val modified = Process("git status --porcelain").lineStream.nonEmpty
date + "-" + hash + (if (modified) "-dirty" else "")
}
ThisBuild / useCoursier := false
ThisBuild / version := ToolkitVersion
lazy val commonSettings = Seq(
organization := "com.editasmedicine",
organizationName := "Editas Medicine Inc.",
organizationHomepage := Some(url("http://www.editasmedicine.com/")),
homepage := Some(url("https://bitbucket.org/editascomputationalbiology/")),
startYear := Some(2017),
scalaVersion := "2.13.8",
scalacOptions += "-target:jvm-1.8",
autoAPIMappings := true,
version := ToolkitVersion,
resolvers += Resolver.jcenterRepo,
resolvers += Resolver.sonatypeRepo("public"),
resolvers += Resolver.mavenLocal,
resolvers += Resolver.file("ivy-local", new File("~/.ivy2/local")),
resolvers += "BroadSnapshots" at "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/",
shellPrompt := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
updateOptions := updateOptions.value.withCachedResolution(true),
Test / testOptions += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
Test / testOptions += Tests.Argument("-oDF"),
Test / javaOptions += "-Xmx1G",
Test / fork := true
) ++ Defaults.coreDefaultSettings
lazy val assemblySettings = Seq(
// Assembly related settings
assembly / assemblyJarName := s"${name.value}.jar",
assembly / test := {},
assembly / assemblyMergeStrategy := {
case PathList("log4j2.xml") => MergeStrategy.first
case x =>
val oldStrategy = (assembly / assemblyMergeStrategy).value
oldStrategy(x)
}
)
////////////////////////////////////////////////////////////////////////////////////////////////
// commons project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val commons = Project(id="commons", base=file("commons"))
.settings(commonSettings: _*)
.settings(description := "Utility and base classes used across projects.")
.settings(libraryDependencies ++= Seq(
"org.scalatest" %% "scalatest" % "3.1.3" % "test->*" excludeAll ExclusionRule(organization="org.junit", name="junit"),
"com.fulcrumgenomics" %% "sopt" % "1.1.0",
"com.fulcrumgenomics" %% "commons" % "1.4.0",
"com.fulcrumgenomics" %% "fgbio" % "2.0.0" excludeAll(htsjdkAndPicardExcludes:_*),
"com.beachape" %% "enumeratum" % "1.7.0",
"com.github.samtools" % "htsjdk" % "2.24.1" excludeAll(htsjdkAndPicardExcludes: _*)
),
)
.disablePlugins(AssemblyPlugin)
////////////////////////////////////////////////////////////////////////////////////////////////
// Aligner project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val calitas = Project(id="calitas", base=file("calitas"))
.settings(commonSettings: _*)
.settings(assemblySettings: _*)
.settings(description := "Library and command line tools for CALITAS.")
.dependsOn(commons % "compile->compile;test->test")
lazy val root = Project(id="calitas-and-commons", base=file("."))
.settings(commonSettings:_*)
.aggregate(commons, calitas)
.disablePlugins(AssemblyPlugin)