Merge pull request #18 from Rappsilber-Laboratory/1.2.28

1.2.34

doc/xiFDR.bat

@@ -0,0 +1,7 @@
+SET mypath=%~dp0
+java -jar %mypath%xiFDR-1.0.22-jar-with-dependencies.jar
+if NOT ["%errorlevel%"]==["0"] (
+    pause
+    exit /b %errorlevel%
+)
+exit

pom.xml

@@ -3,14 +3,9 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.rappsilberlab</groupId>
     <artifactId>xiFDR</artifactId>
-    <version>1.0.22</version>
+    <version>1.2.34</version>
     <packaging>jar</packaging>
     <dependencies>
-        <dependency>
-            <groupId>mzidentml</groupId>
-            <artifactId>jmzidentml</artifactId>
-            <version>1.1.3</version>
-        </dependency>
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
@@ -45,6 +40,64 @@
             <artifactId>CSV</artifactId>
             <version>1.0-SNAPSHOT</version>
         </dependency>
+        <dependency>
+            <groupId>rappsilber</groupId>
+            <artifactId>XiSearch</artifactId>
+            <version>1.6.749</version>
+        </dependency>
+        <dependency>
+            <groupId>org.rappsilber</groupId>
+            <artifactId>XLMOD</artifactId>
+            <version>1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>uk.ac.liv</groupId>
+            <artifactId>mzidlib</artifactId>
+            <version>1.7</version>
+        </dependency>
+        <dependency>
+          <groupId>postgresql</groupId>
+          <artifactId>postgresql</artifactId>
+          <version>9.1-901-1.jdbc4</version>
+        </dependency>
+        <dependency>
+          <groupId>uk.ac.ebi.jmzidml</groupId>
+          <artifactId>jmzidentml</artifactId>
+          <version>1.2.5-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+          <groupId>uk.ac.liv</groupId>
+          <artifactId>mzidlib</artifactId>
+          <version>1.7</version>
+           <exclusions>
+            <exclusion>
+              <groupId>net.jimmc</groupId>
+              <artifactId>jshortcut</artifactId>
+            </exclusion>
+            <exclusion>
+              <groupId>au.com.bytecode</groupId>
+              <artifactId>opencsv</artifactId>
+            </exclusion>
+             <exclusion>
+               <groupId>org.xerial</groupId>
+               <artifactId>sqlite-jdbc</artifactId>
+             </exclusion>
+             <exclusion>
+               <groupId>de.proteinms.xtandemparser</groupId>
+               <artifactId>xtandem-parser</artifactId>
+             </exclusion>
+           </exclusions>     
+        </dependency>
+        <dependency>
+            <groupId>com.sun.xml.bind</groupId>
+            <artifactId>jaxb-impl</artifactId>
+            <version>2.2.7</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.woodstox</groupId>
+            <artifactId>woodstox-core</artifactId>
+            <version>6.0.0.pr2</version>
+        </dependency>
     </dependencies>
     <build>
 	<plugins>
@@ -85,4 +138,7 @@
         <maven.compiler.source>1.7</maven.compiler.source>
         <maven.compiler.target>1.7</maven.compiler.target>
     </properties>
+    <description>Application for FDR estimation cross-linking massspectrometry data
+</description>
+    <name>xiFDR-1.2.34</name>
 </project>