Bump to 0.9.0-RC1

1ef9b735 · pjvan_thof · 6a6c8673 · 1ef9b735 · 1ef9b735 · 1ef9b735
Commit 1ef9b735 authored Apr 25, 2017 by pjvan_thof
26 changed files
--- 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>


--- 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>
    

--- 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>
    

--- 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>


--- 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>


--- 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>
    

--- 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>


--- 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>


--- 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>

--- 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>

--- 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

--- 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>
    

--- 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>

--- 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>


--- 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>
    

--- 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>

--- 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>


--- 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>
    

--- 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>


--- 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>
    

--- 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>
    

--- 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>

--- 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>
    

--- 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>


--- 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>


--- 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>