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Helper scripts to run an ADAM Console. #231

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Apr 29, 2014
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Helper scripts to run an ADAM Console. #231

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8 changes: 8 additions & 0 deletions scripts/adam-console.sh
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#!/bin/bash

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
PROJECT_ROOT="$DIR/.."
VERSION=$(grep "<version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
ADAM_JAR=$PROJECT_ROOT/adam-cli/target/adam-$VERSION.jar
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You could also just do ADAM_JAR=$PROJECT_ROOT/adam-cli/target/adam-?.?.?-SNAPSHOT.jar instead of grabbing the version from the pom file.

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Yeah, but I've noticed that my target subdirectory accumulates multiple versions as time goes on.


SPARK_CLASSPATH=$ADAM_JAR spark-shell -i:$DIR/scala-console.scala
15 changes: 15 additions & 0 deletions scripts/scala-console.scala
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import org.bdgenomics.adam.avro.ADAMRecord
import org.bdgenomics.adam.avro.ADAMNucleotideContigFragment
import org.bdgenomics.adam.avro.ADAMPileup
import org.bdgenomics.adam.avro.ADAMNestedPileup
import org.bdgenomics.adam.avro.ADAMContig
import org.bdgenomics.adam.avro.ADAMVariant
import org.bdgenomics.adam.avro.VariantCallingAnnotations
import org.bdgenomics.adam.avro.ADAMGenotype
import org.bdgenomics.adam.avro.VariantEffect
import org.bdgenomics.adam.avro.ADAMDatabaseVariantAnnotation
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.rdd.ADAMContext
import org.bdgenomics.adam.rdd.ADAMContext._
println("\nYou can call ADAMContext methods on sc")
println("Load a file using: sc.adamLoad(\"<Path to file>\");")