diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar b/settings/repository/edu.mit.broad/picard-private-parts-1954.jar
similarity index 88%
rename from settings/repository/edu.mit.broad/picard-private-parts-1941.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1954.jar
index 760db5cb8..67637d3d9 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1954.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml
new file mode 100644
index 000000000..c702fd6e5
--- /dev/null
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1954" status="integration" publication="20110712113100" />
+</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
similarity index 100%
rename from settings/repository/edu.mit.broad/picard-private-parts-1941.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
diff --git a/settings/repository/net.sf/picard-1.47.869.jar b/settings/repository/net.sf/picard-1.48.889.jar
similarity index 87%
rename from settings/repository/net.sf/picard-1.47.869.jar
rename to settings/repository/net.sf/picard-1.48.889.jar
index d277fd217..1b725dde5 100644
Binary files a/settings/repository/net.sf/picard-1.47.869.jar and b/settings/repository/net.sf/picard-1.48.889.jar differ
diff --git a/settings/repository/net.sf/picard-1.48.889.xml b/settings/repository/net.sf/picard-1.48.889.xml
new file mode 100644
index 000000000..877687930
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.48.889.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.48.889" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.47.869.xml b/settings/repository/net.sf/picard-1.48.889.xml~
similarity index 100%
rename from settings/repository/net.sf/picard-1.47.869.xml
rename to settings/repository/net.sf/picard-1.48.889.xml~
diff --git a/settings/repository/net.sf/sam-1.47.869.xml b/settings/repository/net.sf/sam-1.47.869.xml
deleted file mode 100644
index 1b76fe2f9..000000000
--- a/settings/repository/net.sf/sam-1.47.869.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.47.869" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.47.869.jar b/settings/repository/net.sf/sam-1.48.889.jar
similarity index 91%
rename from settings/repository/net.sf/sam-1.47.869.jar
rename to settings/repository/net.sf/sam-1.48.889.jar
index 933b9cfd6..33ae4aa7d 100644
Binary files a/settings/repository/net.sf/sam-1.47.869.jar and b/settings/repository/net.sf/sam-1.48.889.jar differ
diff --git a/settings/repository/net.sf/sam-1.48.889.xml b/settings/repository/net.sf/sam-1.48.889.xml
new file mode 100644
index 000000000..8046a0c02
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.48.889.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.48.889" status="release" />
+</ivy-module>