Merge branch 'core' into bioinformatics
diff --git a/pom.xml b/pom.xml
index 80c52f6..ba2f639 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,9 +11,9 @@
<!-- ##### For each branch, change ${edition} below -->
<artifactId>taverna-commandline-${edition}</artifactId>
- <name>Taverna Command Line Tool Core</name>
+ <name>Taverna Command Line Utility Bioinformatics</name>
<properties>
- <edition>core</edition>
+ <edition>bioinformatics</edition>
<!-- ######## -->
<raven.app.name>taverna-cmd-${edition}-${project.version}-${buildNumber}</raven.app.name>
@@ -40,7 +40,6 @@
<scope>test</scope>
</dependency>
- <!--
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>bioinformatics-activities</artifactId>
@@ -61,7 +60,6 @@
<version>${t2.activities.version}</version>
<scope>test</scope>
</dependency>
- -->
<dependency>
<groupId>net.sf.taverna.t2.component</groupId>
@@ -187,7 +185,6 @@
<!-- generated with workbench-distro/src/main/python/generateArtifactItems.py -->
-
<artifactItem>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
@@ -254,16 +251,86 @@
<artifactItem>
<groupId>xerces</groupId>
<artifactId>xmlParserAPIs</artifactId>
- <version>2.2.1</version>
- <type>pom</type>
- <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.2.1</outputDirectory>
+ <version>2.0.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.0.2</outputDirectory>
</artifactItem>
<artifactItem>
<groupId>xerces</groupId>
<artifactId>xmlParserAPIs</artifactId>
- <version>2.2.1</version>
+ <version>2.0.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-jaxrpc</artifactId>
+ <version>1.4</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-jaxrpc/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-jaxrpc</artifactId>
+ <version>1.4</version>
<type>jar</type>
- <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.2.1</outputDirectory>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-jaxrpc/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-ant</artifactId>
+ <version>1.4</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-ant/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-ant</artifactId>
+ <version>1.4</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-ant/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-saaj</artifactId>
+ <version>1.4</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-saaj/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>axis</groupId>
+ <artifactId>axis-saaj</artifactId>
+ <version>1.4</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/axis/axis-saaj/1.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>activation</groupId>
+ <artifactId>activation</artifactId>
+ <version>1.0.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/activation/activation/1.0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>activation</groupId>
+ <artifactId>activation</artifactId>
+ <version>1.0.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/activation/activation/1.0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>stax</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/stax/stax-api/1.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>stax</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/stax/stax-api/1.0</outputDirectory>
</artifactItem>
<artifactItem>
<groupId>commons-codec</groupId>
@@ -280,6 +347,20 @@
<outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.3</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>1.3.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-io/commons-io/1.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>1.3.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-io/commons-io/1.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.4</version>
@@ -293,7 +374,20 @@
<type>pom</type>
<outputDirectory>${project.build.directory}/repository/org/slf4j/slf4j-log4j12/1.6.4</outputDirectory>
</artifactItem>
-
+ <artifactItem>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.9</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-configuration/commons-configuration/1.9</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.9</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-configuration/commons-configuration/1.9</outputDirectory>
+ </artifactItem>
<artifactItem>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
@@ -311,6 +405,20 @@
<artifactItem>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
+ <version>3.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-collections/commons-collections/3.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-collections</groupId>
+ <artifactId>commons-collections</artifactId>
+ <version>3.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-collections/commons-collections/3.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-collections</groupId>
+ <artifactId>commons-collections</artifactId>
<version>2.0</version>
<type>jar</type>
<outputDirectory>${project.build.directory}/repository/commons-collections/commons-collections/2.0</outputDirectory>
@@ -337,6 +445,48 @@
<outputDirectory>${project.build.directory}/repository/commons-collections/commons-collections/2.1.1</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>arq</artifactId>
+ <version>2.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/arq/2.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>arq</artifactId>
+ <version>2.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/arq/2.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>iri</artifactId>
+ <version>0.8</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/iri/0.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>iri</artifactId>
+ <version>0.8</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/iri/0.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>jena</artifactId>
+ <version>2.6.4</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/jena/2.6.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.hp.hpl.jena</groupId>
+ <artifactId>jena</artifactId>
+ <version>2.6.4</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/hp/hpl/jena/jena/2.6.4</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.1.10</version>
@@ -351,6 +501,34 @@
<outputDirectory>${project.build.directory}/repository/com/sun/xml/bind/jaxb-impl/2.1.10</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.1.6</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/sun/xml/bind/jaxb-impl/2.1.6</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.1.6</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/sun/xml/bind/jaxb-impl/2.1.6</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.ibm.icu</groupId>
+ <artifactId>icu4j</artifactId>
+ <version>3.8</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/ibm/icu/icu4j/3.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.ibm.icu</groupId>
+ <artifactId>icu4j</artifactId>
+ <version>3.8</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/ibm/icu/icu4j/3.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
<version>2.6.1</version>
@@ -436,6 +614,20 @@
</artifactItem>
<artifactItem>
<groupId>xerces</groupId>
+ <artifactId>xerces</artifactId>
+ <version>2.0.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xerces/2.0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>xerces</groupId>
+ <artifactId>xerces</artifactId>
+ <version>2.0.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xerces/2.0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.8.1</version>
<type>jar</type>
@@ -547,6 +739,20 @@
<outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.6.1</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>xerces</groupId>
+ <artifactId>xmlParserAPIs</artifactId>
+ <version>2.2.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.2.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>xerces</groupId>
+ <artifactId>xmlParserAPIs</artifactId>
+ <version>2.2.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/xerces/xmlParserAPIs/2.2.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.0</version>
@@ -603,6 +809,20 @@
<outputDirectory>${project.build.directory}/repository/commons-pool/commons-pool/1.3</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>commons-pool</groupId>
+ <artifactId>commons-pool</artifactId>
+ <version>1.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-pool/commons-pool/1.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-pool</groupId>
+ <artifactId>commons-pool</artifactId>
+ <version>1.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-pool/commons-pool/1.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.1-beta-9</version>
@@ -633,6 +853,20 @@
<artifactItem>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
+ <version>2.3</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-lang/commons-lang/2.3</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.3</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-lang/commons-lang/2.3</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
<version>2.2</version>
<type>pom</type>
<outputDirectory>${project.build.directory}/repository/commons-lang/commons-lang/2.2</outputDirectory>
@@ -673,6 +907,20 @@
<outputDirectory>${project.build.directory}/repository/commons-lang/commons-lang/1.0</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>commons-discovery</groupId>
+ <artifactId>commons-discovery</artifactId>
+ <version>0.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-discovery/commons-discovery/0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-discovery</groupId>
+ <artifactId>commons-discovery</artifactId>
+ <version>0.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-discovery/commons-discovery/0.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>uk.org.mygrid.resources.mimeutil</groupId>
<artifactId>mime-util</artifactId>
<version>2.1.2-3</version>
@@ -729,6 +977,20 @@
<outputDirectory>${project.build.directory}/repository/log4j/log4j/1.2.12</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>stax</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/stax/stax-api/1.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>stax</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/stax/stax-api/1.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.4</version>
@@ -771,6 +1033,34 @@
<outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.2</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>antlr</groupId>
+ <artifactId>antlr</artifactId>
+ <version>2.7.5</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/antlr/antlr/2.7.5</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>antlr</groupId>
+ <artifactId>antlr</artifactId>
+ <version>2.7.5</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/antlr/antlr/2.7.5</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-beanutils</groupId>
+ <artifactId>commons-beanutils-core</artifactId>
+ <version>1.7.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-beanutils/commons-beanutils-core/1.7.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-beanutils</groupId>
+ <artifactId>commons-beanutils-core</artifactId>
+ <version>1.7.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-beanutils/commons-beanutils-core/1.7.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.4</version>
@@ -1081,6 +1371,20 @@
<artifactItem>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
+ <version>1.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-dbcp/commons-dbcp/1.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-dbcp</groupId>
+ <artifactId>commons-dbcp</artifactId>
+ <version>1.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-dbcp/commons-dbcp/1.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-dbcp</groupId>
+ <artifactId>commons-dbcp</artifactId>
<version>1.2.2</version>
<type>jar</type>
<outputDirectory>${project.build.directory}/repository/commons-dbcp/commons-dbcp/1.2.2</outputDirectory>
@@ -1177,6 +1481,13 @@
<outputDirectory>${project.build.directory}/repository/org/apache/apache/7</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>org.apache</groupId>
+ <artifactId>apache</artifactId>
+ <version>9</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/apache/9</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>2.11.0</version>
@@ -1205,6 +1516,20 @@
<outputDirectory>${project.build.directory}/repository/org/apache/jena/jena-iri/1.0.0</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ <version>2.0.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/lucene/lucene-core/2.0.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ <version>2.0.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/lucene/lucene-core/2.0.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>org.apache.xmlbeans</groupId>
<artifactId>xmlbeans</artifactId>
<version>2.3.0</version>
@@ -1228,6 +1553,13 @@
<artifactItem>
<groupId>org.apache.commons</groupId>
<artifactId>commons-parent</artifactId>
+ <version>25</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/commons/commons-parent/25</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-parent</artifactId>
<version>17</version>
<type>pom</type>
<outputDirectory>${project.build.directory}/repository/org/apache/commons/commons-parent/17</outputDirectory>
@@ -1277,6 +1609,20 @@
<artifactItem>
<groupId>org.codehaus.woodstox</groupId>
<artifactId>wstx-asl</artifactId>
+ <version>3.0.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/codehaus/woodstox/wstx-asl/3.0.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>wstx-asl</artifactId>
+ <version>3.0.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/codehaus/woodstox/wstx-asl/3.0.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>wstx-asl</artifactId>
<version>3.2.9</version>
<type>pom</type>
<outputDirectory>${project.build.directory}/repository/org/codehaus/woodstox/wstx-asl/3.2.9</outputDirectory>
@@ -1492,6 +1838,48 @@
<outputDirectory>${project.build.directory}/repository/org/ccil/cowan/tagsoup/tagsoup/0.9.7</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>juh</artifactId>
+ <version>2.3.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/juh/2.3.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>juh</artifactId>
+ <version>2.3.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/juh/2.3.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>jurt</artifactId>
+ <version>2.3.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/jurt/2.3.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>jurt</artifactId>
+ <version>2.3.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/jurt/2.3.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>ridl</artifactId>
+ <version>2.3.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/ridl/2.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.openoffice</groupId>
+ <artifactId>ridl</artifactId>
+ <version>2.3.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/openoffice/ridl/2.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1</version>
@@ -1506,6 +1894,20 @@
<outputDirectory>${project.build.directory}/repository/javax/activation/activation/1.1</outputDirectory>
</artifactItem>
<artifactItem>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/javax/xml/stream/stax-api/1.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>javax.xml.stream</groupId>
+ <artifactId>stax-api</artifactId>
+ <version>1.0</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/javax/xml/stream/stax-api/1.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>1.4</version>
diff --git a/src/main/install4j/taverna-commandline.install4j b/src/main/install4j/taverna-commandline.install4j
index 60a7ad3..36366d6 100644
--- a/src/main/install4j/taverna-commandline.install4j
+++ b/src/main/install4j/taverna-commandline.install4j
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<install4j version="5.1.11" transformSequenceNumber="4">
<directoryPresets config="../../../target/taverna-workbench-dist/taverna.sh" />
- <application name="${compiler:product-name}" distributionSourceDir="" applicationId="6321-5227-3164-0432" mediaDir="../../../target/media" mediaFilePattern="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="taverna-commandline-${compiler:edition}" publisher="myGrid" publisherWeb="http://www.taverna.org.uk/" version="2.5-SNAPSHOT" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="false" macSignature="????" installerName="" javaMinVersion="1.7" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
+ <application name="${compiler:product-name}" distributionSourceDir="" applicationId="0648-0915-0462-4646" mediaDir="../../../target/media" mediaFilePattern="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="taverna-commandline-${compiler:edition}" publisher="myGrid" publisherWeb="http://www.taverna.org.uk/" version="2.5-SNAPSHOT" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="false" macSignature="????" installerName="" javaMinVersion="1.7" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
<languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
<principalLanguage id="en" customLocalizationFile="" />
<additionalLanguages />
diff --git a/src/main/resources/plugins/plugins.xml b/src/main/resources/plugins/plugins.xml
index 1d85405..7cc2090 100644
--- a/src/main/resources/plugins/plugins.xml
+++ b/src/main/resources/plugins/plugins.xml
@@ -33,7 +33,6 @@
</compatibility>
</plugin>
- <!--
<plugin>
<provider>taverna.sf.net</provider>
<identifier>net.sf.taverna.t2.activities.bioinformatics-no-ui</identifier>
@@ -123,7 +122,6 @@
</application>
</compatibility>
</plugin>
- -->
<plugin>
<provider>taverna.sf.net</provider>
