JAL-1766 added a snapshot build of the htsjdk

diff --git a/.classpath b/.classpath
index 0abfdb3..90323de 100644 (file)
--- 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 (file)
--- 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 (file)
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 (executable)
--- 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">