New upstream version 2.18.14+dfsg

<?xml version="1.0" encoding="UTF-8"?>

<classpath>

 <classpathentry kind="src" path="src/java"/>

 <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

 <classpathentry kind="lib" path="lib/testng/testng-5.5-jdk15.jar"/>

 <classpathentry kind="lib" path="lib/ant/bcel-5.2.jar"/>

 <classpathentry kind="output" path="bin"/>

</classpath>

<?xml version="1.0" encoding="UTF-8"?>

<projectDescription>

 <name>picard</name>

 <comment></comment>

 <projects>

 </projects>

 <buildSpec>

 <buildCommand>

 <name>org.eclipse.jdt.core.javabuilder</name>

 <arguments>

 </arguments>

 </buildCommand>

 </buildSpec>

 <natures>

 <nature>org.eclipse.jdt.core.javanature</nature>

 </natures>

</projectDescription>

FROM broadinstitute/java-baseimage

MAINTAINER Broad Institute DSDE <dsde-engineering@broadinstitute.org>

ARG build_command=shadowJar

ARG jar_name=picard.jar

# Install ant, git for building

RUN apt-get update && \

    apt-get --no-install-recommends install -y --force-yes \

        git \

        r-base \

        ant && \

    apt-get clean autoclean && \

    apt-get autoremove -y

WORKDIR /usr/picard

# Build the distribution jar, clean up everything else

RUN ./gradlew shadowJar && \

    mv build/libs/picard.jar picard.jar && \

RUN ./gradlew ${build_command} && \

    mv build/libs/${jar_name} picard.jar && \

    mv src/main/resources/picard/docker_helper.sh docker_helper.sh && \

    ./gradlew clean && \

    rm -rf src && \

    toolVersion = "0.7.5.201505241946"

}

final htsjdkVersion = System.getProperty('htsjdk.version', '2.14.3')

final requiredJavaVersion = "8"

final buildPrerequisitesMessage = "See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard"

// Ensure that we have the right JDK version, a clone of the git repository

def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) {

    // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.

    if (ToolProvider.getSystemToolClassLoader() == null) {

        throw new GradleException(

                "The ClassLoader obtained from the Java ToolProvider is null. "

                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")

    }

    if (!file(".git").isDirectory()) {

        throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "

                + "$buildPrerequisitesMessage")

    }

}

ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage)

final htsjdkVersion = System.getProperty('htsjdk.version', '2.16.1')

// We use a custom shaded build of the NIO library to avoid a regression in the authentication layer.

// GATK does the same, see https://github.com/broadinstitute/gatk/issues/3591

}

dependencies {

    compile('com.intel.gkl:gkl:0.8.2') {

    compile('com.intel.gkl:gkl:0.8.5') {

        exclude module: 'htsjdk'

    }

    compile 'com.google.guava:guava:15.0'

    compile 'org.apache.commons:commons-math3:3.5'

    compile 'com.github.samtools:htsjdk:' + htsjdkVersion

    compile 'org.broadinstitute:barclay:2.0.0'

    compileOnly googleNio

#!/usr/bin/env bash

# This script is used to build and deploy docker images for Picard

if [[ "$1" == "" ]]

then

    echo "Usage: build_push_docker.sh <git-tag>"

    exit 1

fi

declare -r TAG=${1}

declare -r PICARD_TAG=broadinstitute/picard:${TAG}

declare -r PICARD_CLOUD_TAG=us.gcr.io/broad-gotc-prod/picard-cloud:${TAG}

echo "Will build and push the following docker images:"

echo ${PICARD_TAG}

echo ${PICARD_CLOUD_TAG}

read -p "Is this really what you want to do? " -n 1 -r

echo    # (optional) move to a new line

if [[ $REPLY =~ ^[Yy]$ ]]

then

    docker build -t ${PICARD_TAG} --build-arg build_command=shadowJar --build-arg jar_name=picard.jar .

    docker build -t ${PICARD_CLOUD_TAG} --build-arg build_command=cloudJar --build-arg jar_name=picardcloud.jar .

    docker push ${PICARD_TAG}

    gcloud docker -- push ${PICARD_CLOUD_TAG}

fi