Merge pull request #761 from broadinstitute/ks_junction_plugin_local_repo

Adding sysinternals:junction:1.04:exe to local repo.

public/gatk-root/pom.xml

@@ -667,6 +667,38 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-install-plugin</artifactId>
+                <executions>
+                    <!--
+                    The pom for com.pyx4j:maven-junction-plugin:1.0.3 points to
+                    sysinternals:junction:1.04:exe. This file is only hosted in the repo
+                    http://www.pyx4me.com/maven2, and the website keeps going down.
+
+                    This file is only used on windows, but the maven-plugin devs never finished
+                    implementing *plugin* dependency exclusions: http://jira.codehaus.org/browse/MNG-2163
+
+                    Until someone updates or replaces this 2007 plugin with a new plugin using Java 7's Files class,
+                    for now we copy over the artifact just in case the website is unavailable.
+
+                    See also: http://docs.oracle.com/javase/7/docs/api/java/nio/file/Files.html#createSymbolicLink(java.nio.file.Path,%20java.nio.file.Path,%20java.nio.file.attribute.FileAttribute...)
+                    -->
+                    <execution>
+                        <id>install-sysinternals-junction</id>
+                        <goals>
+                            <goal>install-file</goal>
+                        </goals>
+                        <phase>initialize</phase>
+                        <inherited>false</inherited>
+                        <configuration>
+                            <file>${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.exe</file>
+                            <pomFile>${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.pom</pomFile>
+                            <packaging>exe</packaging>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 

public/repo/sysinternals/junction/1.04/junction-1.04.exe.md5

@@ -0,0 +1 @@
+b25b81716aaca69eecd0eedbf7891ad1

public/repo/sysinternals/junction/1.04/junction-1.04.pom

@@ -0,0 +1,15 @@
+<project>
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>sysinternals</groupId>
+  <artifactId>junction</artifactId>
+  <version>1.04</version>
+  <url>http://www.sysinternals.com/Utilities/Junction.html</url>
+  <name>Junction (symbolic links on windows)</name>
+  <description>Directory symbolic links are known as NTFS junctions in Windows.</description>
+  <licenses>
+    <license>
+        <name>SYSINTERNALS SOFTWARE LICENSE</name>
+        <url>http://www.sysinternals.com/Licensing.html</url>
+    </license>
+  </licenses>
+</project>

public/repo/sysinternals/junction/1.04/junction-1.04.pom.md5

@@ -0,0 +1 @@
+253b197c9831aef9e275a751a464e332