From 1ef9b7350aa30396afe761bb50b250332fbe0bb7 Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Tue, 25 Apr 2017 15:50:39 +0200
Subject: [PATCH] Bump to 0.9.0-RC1

---
 bam2wig/pom.xml                 | 2 +-
 bammetrics/pom.xml              | 2 +-
 basty/pom.xml                   | 2 +-
 biopet-core/pom.xml             | 6 +++---
 biopet-extensions/pom.xml       | 2 +-
 biopet-package/pom.xml          | 2 +-
 biopet-tools-extensions/pom.xml | 2 +-
 biopet-tools-package/pom.xml    | 2 +-
 biopet-tools/pom.xml            | 2 +-
 biopet-utils/pom.xml            | 2 +-
 bump-version.sh                 | 3 +--
 carp/pom.xml                    | 2 +-
 docs/examples/pom.xml           | 2 +-
 external-example/pom.xml        | 8 ++++----
 flexiprep/pom.xml               | 2 +-
 gears/pom.xml                   | 2 +-
 generate-indexes/pom.xml        | 2 +-
 gentrap/pom.xml                 | 2 +-
 gwas-test/pom.xml               | 2 +-
 kopisu/pom.xml                  | 2 +-
 mapping/pom.xml                 | 2 +-
 pom.xml                         | 2 +-
 sage/pom.xml                    | 2 +-
 shiva/pom.xml                   | 2 +-
 tinycap/pom.xml                 | 2 +-
 toucan/pom.xml                  | 2 +-
 26 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/bam2wig/pom.xml b/bam2wig/pom.xml
index 92d2cfc49..9d9254546 100644
--- a/bam2wig/pom.xml
+++ b/bam2wig/pom.xml
@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
 
diff --git a/bammetrics/pom.xml b/bammetrics/pom.xml
index e4246a3c9..0290b3de2 100644
--- a/bammetrics/pom.xml
+++ b/bammetrics/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/basty/pom.xml b/basty/pom.xml
index 9960384d2..08f37807f 100644
--- a/basty/pom.xml
+++ b/basty/pom.xml
@@ -31,7 +31,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/biopet-core/pom.xml b/biopet-core/pom.xml
index 9fbcc9a3d..bbcbee94d 100644
--- a/biopet-core/pom.xml
+++ b/biopet-core/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -38,7 +38,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue</artifactId>
-            <version>3.6</version>
+            <version>0.9.0</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.broadinstitute.gatk</groupId>
@@ -49,7 +49,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue-extensions-public</artifactId>
-            <version>3.6</version>
+            <version>0.9.0</version>
         </dependency>
     </dependencies>
 
diff --git a/biopet-extensions/pom.xml b/biopet-extensions/pom.xml
index 992f94278..f73b67abd 100644
--- a/biopet-extensions/pom.xml
+++ b/biopet-extensions/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/biopet-package/pom.xml b/biopet-package/pom.xml
index 25eac4463..a1062fbf7 100644
--- a/biopet-package/pom.xml
+++ b/biopet-package/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/biopet-tools-extensions/pom.xml b/biopet-tools-extensions/pom.xml
index e100fd4e5..b106d7c38 100644
--- a/biopet-tools-extensions/pom.xml
+++ b/biopet-tools-extensions/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/biopet-tools-package/pom.xml b/biopet-tools-package/pom.xml
index 6692a12f6..ee01a311d 100644
--- a/biopet-tools-package/pom.xml
+++ b/biopet-tools-package/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/biopet-tools/pom.xml b/biopet-tools/pom.xml
index 7ce521540..9722f1a71 100644
--- a/biopet-tools/pom.xml
+++ b/biopet-tools/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
diff --git a/biopet-utils/pom.xml b/biopet-utils/pom.xml
index 3e8d09950..4261b8c6e 100644
--- a/biopet-utils/pom.xml
+++ b/biopet-utils/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
diff --git a/bump-version.sh b/bump-version.sh
index 120791235..029d8627d 100755
--- a/bump-version.sh
+++ b/bump-version.sh
@@ -21,8 +21,7 @@ if [ ! $1 ] ; then
     exit 1
 fi
 
-for POM in `find $DIR -name "pom.xml"`
 do
-	mvn -f $POM versions:set -DnewVersion=$1 -DgenerateBackupPoms=false
+	mvn -f $DIR/pom.xml versions:set -DnewVersion=$1 -DgenerateBackupPoms=false
 done
 
diff --git a/carp/pom.xml b/carp/pom.xml
index 5d4760e2a..4e6254136 100644
--- a/carp/pom.xml
+++ b/carp/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/docs/examples/pom.xml b/docs/examples/pom.xml
index e946e8561..a88ca8b68 100644
--- a/docs/examples/pom.xml
+++ b/docs/examples/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>path.to.your</groupId>
     <artifactId>MyProject</artifactId>
-    <version>0.8.0-SNAPSHOT</version>
+    <version>0.9.0</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
diff --git a/external-example/pom.xml b/external-example/pom.xml
index 94762d4f3..ccf0efd15 100644
--- a/external-example/pom.xml
+++ b/external-example/pom.xml
@@ -27,7 +27,7 @@
     <artifactId>ExternalExample</artifactId>
 
     <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
-    <version>0.8.0-SNAPSHOT</version>
+    <version>0.9.0</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -56,19 +56,19 @@
             <artifactId>BiopetCore</artifactId>
 
             <!--TODO: replace version of pipeline to a fixed version -->
-            <version>0.9.0-SNAPSHOT</version>
+            <version>0.9.0-RC1</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>BiopetExtensions</artifactId>
-            <version>0.9.0-SNAPSHOT</version>
+            <version>0.9.0-RC1</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Shiva</artifactId>
 
             <!--TODO: replace version of pipeline to a fixed version -->
-            <version>0.9.0-SNAPSHOT</version>
+            <version>0.9.0-RC1</version>
         </dependency>
     </dependencies>
 
diff --git a/flexiprep/pom.xml b/flexiprep/pom.xml
index 031317223..3aa7b432f 100644
--- a/flexiprep/pom.xml
+++ b/flexiprep/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/gears/pom.xml b/gears/pom.xml
index 9eb7b6a1f..22d14cab9 100644
--- a/gears/pom.xml
+++ b/gears/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
diff --git a/generate-indexes/pom.xml b/generate-indexes/pom.xml
index fc8a67d97..2d651f990 100644
--- a/generate-indexes/pom.xml
+++ b/generate-indexes/pom.xml
@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
 
diff --git a/gentrap/pom.xml b/gentrap/pom.xml
index 1f60a5871..c723f91b8 100644
--- a/gentrap/pom.xml
+++ b/gentrap/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/gwas-test/pom.xml b/gwas-test/pom.xml
index ffd893ac0..190c1c5bc 100644
--- a/gwas-test/pom.xml
+++ b/gwas-test/pom.xml
@@ -26,7 +26,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
 
diff --git a/kopisu/pom.xml b/kopisu/pom.xml
index 66228fc89..91f1ca971 100644
--- a/kopisu/pom.xml
+++ b/kopisu/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/mapping/pom.xml b/mapping/pom.xml
index c6fed7b8c..f6ea3f59f 100644
--- a/mapping/pom.xml
+++ b/mapping/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/pom.xml b/pom.xml
index 31e568a57..e5a844730 100644
--- a/pom.xml
+++ b/pom.xml
@@ -21,7 +21,7 @@
     <groupId>nl.lumc.sasc</groupId>
     <name>Biopet</name>
     <packaging>pom</packaging>
-    <version>0.9.0-SNAPSHOT</version>
+    <version>0.9.0-RC1</version>
     
     <modules>
         <module>gatk</module>
diff --git a/sage/pom.xml b/sage/pom.xml
index 909671172..0f74c4b90 100644
--- a/sage/pom.xml
+++ b/sage/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
diff --git a/shiva/pom.xml b/shiva/pom.xml
index 1fcb40227..63d786a74 100644
--- a/shiva/pom.xml
+++ b/shiva/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/tinycap/pom.xml b/tinycap/pom.xml
index 05e5b0fe4..819433e1a 100644
--- a/tinycap/pom.xml
+++ b/tinycap/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <artifactId>Biopet</artifactId>
         <groupId>nl.lumc.sasc</groupId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/toucan/pom.xml b/toucan/pom.xml
index 7c97d91a9..0f92658e2 100644
--- a/toucan/pom.xml
+++ b/toucan/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.0-RC1</version>
         <relativePath>../</relativePath>
     </parent>
     
-- 
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