[med-svn] [picard-tools] 04/06: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository picard-tools.

commit 4c51b3d4aba1fcf19a144cf797bcbbd854533744
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 10 10:29:19 2016 +0200

    Adapt patches
---
 debian/patches/10-build.xml.patch | 25 ++++++++-----------------
 1 file changed, 8 insertions(+), 17 deletions(-)

diff --git a/debian/patches/10-build.xml.patch b/debian/patches/10-build.xml.patch
index 631c5b6..8d9e09b 100644
--- a/debian/patches/10-build.xml.patch
+++ b/debian/patches/10-build.xml.patch
@@ -4,13 +4,7 @@ Forwarded: not-needed
 Last-Updated: 2016-07-07
 --- a/build.gradle
 +++ b/build.gradle
-@@ -1,5 +1,4 @@
- import javax.tools.ToolProvider
--import org.ajoberstar.grgit.*
- 
- buildscript {
-     repositories {
-@@ -11,13 +10,7 @@
+@@ -12,13 +12,7 @@ plugins {
      id "java"
      id 'maven'
      id 'signing'
@@ -24,8 +18,8 @@ Last-Updated: 2016-07-07
  }
  
  mainClassName = "picard.cmdline.PicardCommandLine"
-@@ -27,22 +20,6 @@
-     mavenCentral()
+@@ -31,22 +25,6 @@ repositories {
+     }
  }
  
 -jacocoTestReport {
@@ -44,10 +38,10 @@ Last-Updated: 2016-07-07
 -    toolVersion = "0.7.5.201505241946"
 -}
 -
+ final htsjdkVersion = System.getProperty('htsjdk.version', '2.6.0')
+ 
  dependencies {
-     compile 'com.google.guava:guava:15.0'
-     compile ('com.github.samtools:htsjdk:2.5.0')
-@@ -54,9 +31,17 @@
+@@ -60,9 +38,18 @@ dependencies {
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -59,6 +53,7 @@ Last-Updated: 2016-07-07
 +    }
 +    return dpkgStdOut.toString().trim().replaceFirst(/(-gradle)?([+]dfsg[.0-9]*)?-[^-]+$/, "")
 +}
++
  final isRelease = Boolean.getBoolean("release")
 -final gitVersion = gitVersion().replaceAll(".dirty", "")
 -version = isRelease ? gitVersion : gitVersion + "-SNAPSHOT"
@@ -67,7 +62,7 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -308,19 +293,3 @@
+@@ -321,19 +308,3 @@ task copyJavadoc(dependsOn: 'javadoc', t
      from 'build/docs/javadoc'
      into "$htmlDir/javadoc"
  }
@@ -91,7 +86,3 @@ Last-Updated: 2016-07-07
 +++ b/gradle.properties
 @@ -0,0 +1 @@
 +rootName=picard
---- /dev/null
-+++ b/settings.gradle
-@@ -0,0 +1 @@
-+rootProject.name = rootName

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