From 1324120c1703a6e0c0bad6a47bc983d6eef8d007 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 14 Mar 2014 10:50:15 -0400
Subject: [PATCH] Unconditionally include all of commons-httpclient in the
 GATK/Queue jars

The maven shade plugin was eliminating a necessary class (IgnoreCookiesSpec)
when packaging the GATK/Queue. Work around this by telling maven to
always package all of commons-httpclient.
---
 public/gatk-package/pom.xml  | 5 +++++
 public/queue-package/pom.xml | 5 +++++
 public/sting-root/pom.xml    | 5 +++++
 3 files changed, 15 insertions(+)

diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 606d9f030..79a55b205 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -43,6 +43,11 @@
             <groupId>commons-logging</groupId>
             <artifactId>commons-logging</artifactId>
         </dependency>
+        <!-- Workaround - depend on commons-httpclient to prevent shade from eliminating IgnoreCookiesSpec class -->
+        <dependency>
+            <groupId>commons-httpclient</groupId>
+            <artifactId>commons-httpclient</artifactId>
+        </dependency>
         <!-- Required for binary-dist assembly, excluded by shade -->
         <dependency>
             <groupId>${project.groupId}</groupId>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 89b547b2f..e90222e0b 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -67,6 +67,11 @@
             <groupId>net.sf.snpeff</groupId>
             <artifactId>snpeff</artifactId>
         </dependency>
+        <!-- Workaround - depend on commons-httpclient to prevent shade from eliminating IgnoreCookiesSpec class -->
+        <dependency>
+            <groupId>commons-httpclient</groupId>
+            <artifactId>commons-httpclient</artifactId>
+        </dependency>
         <!-- Required for binary-dist assembly, excluded by shade -->
         <dependency>
             <groupId>${project.groupId}</groupId>
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 5b3dfe43b..00788c94b 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -188,6 +188,11 @@
                 <artifactId>commons-collections</artifactId>
                 <version>3.2.1</version>
             </dependency>
+            <dependency>
+                <groupId>commons-httpclient</groupId>
+                <artifactId>commons-httpclient</artifactId>
+                <version>3.1</version>
+            </dependency>
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-math</artifactId>