Skip to content
This repository was archived by the owner on Nov 28, 2020. It is now read-only.

2.12 scala upgrade #201

Open
agaszmurlo wants to merge 2 commits into
base: master
Choose a base branch
from
Open

2.12 scala upgrade #201

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b1205ec
dependencies upgrade
agaszmurlo Aug 12, 2020
ba87f07
fixing dependencies
agaszmurlo Aug 12, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 15 additions & 17 deletions build.sbt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ lazy val sparkVersion = Properties.envOrElse("SPARK_VERSION", DEFAULT_SPARK_2_VE

version := s"0.6.0-spark-${sparkVersion}"
organization := "org.biodatageeks"
scalaVersion := "2.11.8"
scalaVersion := "2.12.12"


val DEFAULT_HADOOP_VERSION = "2.6.5"
Expand All @@ -20,34 +20,32 @@ dependencyOverrides += "com.google.guava" % "guava" % "15.0"

libraryDependencies += "org.seqdoop" % "hadoop-bam" % "7.10.0"
libraryDependencies += "org.apache.hadoop" % "hadoop-client" % hadoopVersion
libraryDependencies += "org.apache.spark" % "spark-core_2.11" % sparkVersion
libraryDependencies += "org.apache.spark" % "spark-sql_2.11" % sparkVersion
libraryDependencies += "org.apache.spark" % "spark-core_2.12" % sparkVersion
libraryDependencies += "org.apache.spark" % "spark-sql_2.12" % sparkVersion
libraryDependencies += "org.apache.spark" %% "spark-hive" % sparkVersion
libraryDependencies += "org.apache.spark" %% "spark-hive-thriftserver" % "2.4.0"
libraryDependencies += "com.holdenkarau" % "spark-testing-base_2.11" % "2.4.0_0.11.0" % "test" excludeAll ExclusionRule(organization = "javax.servlet") excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "org.bdgenomics.adam" %% "adam-core-spark2" % "0.25.0"
libraryDependencies += "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.25.0"
libraryDependencies += "org.bdgenomics.adam" %% "adam-cli-spark2" % "0.25.0"
libraryDependencies += "org.scala-lang" % "scala-library" % "2.11.8"
libraryDependencies += "com.holdenkarau" % "spark-testing-base_2.12" % "2.4.3_0.14.0" % "test" excludeAll ExclusionRule(organization = "javax.servlet") excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "org.bdgenomics.adam" %% "adam-core-spark2" % "0.27.0"
libraryDependencies += "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.27.0"
libraryDependencies += "org.bdgenomics.adam" %% "adam-cli-spark2" % "0.27.0"
libraryDependencies += "org.scala-lang" % "scala-library" % scalaVersion.toString()
libraryDependencies += "org.rogach" %% "scallop" % "3.1.2"
//libraryDependencies += "org.apache.logging.log4j" % "log4j-slf4j-impl" % "2.11.1"
//libraryDependencies += "org.hammerlab.bdg-utils" %% "cli" %
libraryDependencies += "org.bdgenomics.utils" % "utils-metrics-spark2_2.11" % "0.2.16"
libraryDependencies += "org.bdgenomics.utils" % "utils-metrics-spark2_2.12" % "0.2.16"
libraryDependencies += "com.github.samtools" % "htsjdk" % "2.19.0"
libraryDependencies += "ch.cern.sparkmeasure" %% "spark-measure" % "0.13" excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "ch.cern.sparkmeasure" %% "spark-measure" % "0.16" excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "org.broadinstitute" % "gatk-native-bindings" % "1.0.0" excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "org.apache.logging.log4j" % "log4j-core" % "2.11.0"
libraryDependencies += "org.apache.logging.log4j" % "log4j-api" % "2.11.0"
libraryDependencies += "org.apache.logging.log4j" % "log4j-core" % "2.12.1"
libraryDependencies += "org.apache.logging.log4j" % "log4j-api" % "2.12.1"
libraryDependencies += "com.intel.gkl" % "gkl" % "0.8.5-1-darwin-SNAPSHOT"
libraryDependencies += "com.intel.gkl" % "gkl" % "0.8.5-1-linux-SNAPSHOT"
libraryDependencies += "org.hammerlab.bam" %% "load" % "1.2.0-M1"
//libraryDependencies += "org.hammerlab.bam" %% "load" % "1.2.0-M1"
libraryDependencies += "de.ruedigermoeller" % "fst" % "2.57"
libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.7"
libraryDependencies += "org.eclipse.jetty" % "jetty-servlet" % "9.3.24.v20180605"
libraryDependencies += "org.apache.derby" % "derbyclient" % "10.14.2.0"
libraryDependencies += "org.biodatageeks" % "bdg-performance_2.11" % "0.2-SNAPSHOT" excludeAll (ExclusionRule("org.apache.hadoop"))
libraryDependencies += "org.biodatageeks" % "bdg-performance_2.11" % "0.2-SNAPSHOT" excludeAll (ExclusionRule("org.apache.hadoop"), ExclusionRule("org.apache.spark"), ExclusionRule("org.rogach"), ExclusionRule("com.fasterxml.jackson"), ExclusionRule("ch.cern.sparkmeasure"))
libraryDependencies += "org.disq-bio" % "disq" % "0.3.3"
libraryDependencies += "io.projectglow" %% "glow" % "0.1.2"
libraryDependencies += "io.projectglow" %% "glow" % "0.5.0"
libraryDependencies += "com.github.ichoran" %% "thyme" % "0.1.2-SNAPSHOT"

avroSpecificSourceDirectories in Compile += (sourceDirectory in Compile).value / "avro/input"
Expand Down
7 changes: 0 additions & 7 deletions src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -98,13 +98,6 @@ trait BDGAlignFileReaderWriter [T <: BDGAlignInputFormat]{
.newAPIHadoopFile[LongWritable, SAMRecordWritable, T](path)
.map(r => r._2.get())
}
case "sparkbam" => {
import spark_bam._, hammerlab.path._
val bamPath = Path(resolvedPath)
spark
.sparkContext
.loadReads(bamPath)
}

case "disq" => {
import org.disq_bio.disq.HtsjdkReadsRddStorage
Expand Down
Loading