From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 8 Jun 2015 10:47:44 +0000 (+0100)
Subject: JAL-1766 added a snapshot build of the htsjdk
X-Git-Tag: Release_2_10_0~296^2~145
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=694a4734e2f664aeb8075e6af93d56e90135ad3e

JAL-1766 added a snapshot build of the htsjdk
---

diff --git a/.classpath b/.classpath
index 0abfdb3..90323de 100644
--- a/.classpath
+++ b/.classpath
@@ -51,6 +51,7 @@
 	<classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
 	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
 	<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="lib/htsjdk-1.120-SNAPSHOT.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
 	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index bbef868..95e987d 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -45,6 +45,9 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
+lib/htsjdk-1.120-SNAPSHOT.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+
+
 Additional dependencies
 
 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
diff --git a/lib/htsjdk-1.120-SNAPSHOT.jar b/lib/htsjdk-1.120-SNAPSHOT.jar
new file mode 100644
index 0000000..be2be05
Binary files /dev/null and b/lib/htsjdk-1.120-SNAPSHOT.jar differ
diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index 64f42cd..b65fc3b 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2342,6 +2342,58 @@ and any path to a file to save to the file]]></string>
 							</property>
 						</object>
 					</method>
+					<method name="addElement">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab93">
+							<property name="belongsToUninstallPhase">
+								<boolean>false</boolean>
+							</property>
+							<property name="rollbackEnabledCancel">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledError">
+								<boolean>true</boolean>
+							</property>
+							<property name="ruleExpression">
+								<string><![CDATA[]]></string>
+							</property>
+							<property name="unixPermissions">
+								<string><![CDATA[664]]></string>
+							</property>
+							<property name="sourceName">
+								<string><![CDATA[htsjdk-1.120-SNAPSHOT.jar]]></string>
+							</property>
+							<property name="overrideUnixPermissions">
+								<boolean>false</boolean>
+							</property>
+							<property name="sourcePath">
+								<string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+							</property>
+							<property name="shouldUninstall">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledCancel">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledError">
+								<boolean>true</boolean>
+							</property>
+							<property name="destinationName">
+								<string><![CDATA[htsjdk-1.120-SNAPSHOT.jar]]></string>
+							</property>
+							<property name="fileSize">
+								<long>16046</long>
+							</property>
+							<property name="macBinary">
+								<boolean>false</boolean>
+							</property>
+							<property name="targetCheckKind">
+								<int>0</int>
+							</property>
+							<property name="ruleExpression">
+								<string><![CDATA[]]></string>
+							</property>
+						</object>
+					</method>
 				</object>
 			</property>
 			<property name="rulesFailedMessage">
@@ -6726,6 +6778,7 @@ and any path to a file to read from that file]]></string>
 										<object refID="841f46efeefab93"/>
 										<object refID="9a1f46efeefab93"/>
 										<object refID="1936efeefab93"/>
+										<object refID="1000ddddfab93"/>
 										
 										<object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
 											<property name="belongsToUninstallPhase">
@@ -7305,6 +7358,7 @@ and any path to a file to read from that file]]></string>
 												<object refID="1f46cffffab93"/>
 												<object refID="1f46efeefab93"/>
 												<object refID="1936efeefab93"/>
+												<object refID="1000ddddfab93"/>
 											</visualChildren>
 										</object>
 										<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">