Replaced local drmaa and Jama artifacts with versions from maven central.

Removed unused caliper binary from local repo.

protected/gatk-protected/pom.xml

@@ -31,8 +31,8 @@
         </dependency>
 
         <dependency>
-            <groupId>gov.nist</groupId>
+            <groupId>gov.nist.math</groupId>
-            <artifactId>Jama</artifactId>
+            <artifactId>jama</artifactId>
         </dependency>
 
         <dependency>

public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>com.google.code.caliper</groupId>
-  <artifactId>caliper</artifactId>
-  <name>caliper</name>
-  <version>1.0-SNAPSHOT</version>
-</project>

public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>gov.nist</groupId>
-  <artifactId>Jama</artifactId>
-  <name>Jama</name>
-  <version>1.0.2</version>
-</project>

public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>net.sf.gridscheduler</groupId>
-  <artifactId>drmaa</artifactId>
-  <name>drmaa</name>
-  <version>6.2u5p2</version>
-</project>

public/sting-root/pom.xml

@@ -141,8 +141,8 @@
                 <version>1.6.1</version>
             </dependency>
             <dependency>
-                <groupId>gov.nist</groupId>
+                <groupId>gov.nist.math</groupId>
-                <artifactId>Jama</artifactId>
+                <artifactId>jama</artifactId>
                 <version>1.0.2</version>
             </dependency>
             <dependency>
@@ -201,9 +201,9 @@
                 <version>0.8.1</version>
             </dependency>
             <dependency>
-                <groupId>net.sf.gridscheduler</groupId>
+                <groupId>us.levk</groupId>
-                <artifactId>drmaa</artifactId>
+                <artifactId>drmaa-gridengine</artifactId>
-                <version>6.2u5p2</version>
+                <version>6.2u5</version>
             </dependency>
             <dependency>
                 <groupId>net.sf.snpeff</groupId>

public/sting-utils/pom.xml

@@ -93,8 +93,8 @@
             <artifactId>jets3t</artifactId>
         </dependency>
         <dependency>
-            <groupId>net.sf.gridscheduler</groupId>
+            <groupId>us.levk</groupId>
-            <artifactId>drmaa</artifactId>
+            <artifactId>drmaa-gridengine</artifactId>
         </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>