Working version for ASMS2015

jj-umn · May 29, 2015 · 8274802 · 8274802
1 parent 8516d7b
commit 8274802
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Showing 8 changed files with 431 additions and 73 deletions.
diff --git a/nbactions.xml b/nbactions.xml
@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/iTRAQ_Erwinia.sqlite  /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzid /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzML</exec.args>
+                <exec.args>-Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/GCC2015.sqlite  /Users/jj/gxt/gxt/database/files/006/dataset_6617.dat /Users/jj/gxt/gxt/database/files/006/dataset_6616.dat /Users/jj/gxt/gxt/database/files/006/dataset_6620.dat /Users/jj/gxt/gxt/database/files/006/dataset_6618.dat</exec.args>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>
@@ -24,7 +24,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/iTRAQ_Erwinia.sqlite  /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzid /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzML</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/GCC2015.sqlite  /Users/jj/gxt/gxt/database/files/006/dataset_6617.dat /Users/jj/gxt/gxt/database/files/006/dataset_6616.dat /Users/jj/gxt/gxt/database/files/006/dataset_6620.dat /Users/jj/gxt/gxt/database/files/006/dataset_6618.dat</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
             </properties>
@@ -39,7 +39,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/iTRAQ_Erwinia.sqlite  /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzid /Users/jj/gx/toolsheds/msi/mzid_sqlite/iTRAQ_Erwinia.mzML</exec.args>
+                <exec.args>-Xms4g -classpath %classpath edu.umn.msi.gx.mztosqlite.MzToSQLite -s /Users/jj/Downloads/GCC2015.sqlite  /Users/jj/gxt/gxt/database/files/006/dataset_6617.dat /Users/jj/gxt/gxt/database/files/006/dataset_6616.dat /Users/jj/gxt/gxt/database/files/006/dataset_6620.dat /Users/jj/gxt/gxt/database/files/006/dataset_6618.dat</exec.args>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>

diff --git a/pom.xml b/pom.xml
@@ -97,12 +97,61 @@
 			<groupId>uk.ac.ebi.pride.tools</groupId>
 			<artifactId>pride-wrapper</artifactId>
 			<version>1.2.0</version>
-		</dependency>
+                </dependency>
+                <dependency>
+                    <groupId>com.github.samtools</groupId>
+                    <artifactId>htsjdk</artifactId>
+                    <version>1.130</version>                
+                </dependency>
                 <dependency>
                     <groupId>org.tmatesoft.sqljet</groupId>
                     <artifactId>sqljet</artifactId>
                     <version>1.1.10</version>
                 </dependency>
+            <dependency>
+            <groupId>com.compomics</groupId>
+            <artifactId>utilities</artifactId>
+            <version>3.47.2</version>
+            <exclusions>
+                <exclusion>
+                    <artifactId>commons-math</artifactId>
+                    <groupId>commons-math</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>servlet-api</artifactId>
+                    <groupId>javax.servlet</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>swingx</artifactId>
+                    <groupId>org.swinglabs</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>swing-layout</artifactId>
+                    <groupId>org.swinglabs</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>batik-all</artifactId>
+                    <groupId>batik</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>pdf-transcoder</artifactId>
+                    <groupId>batik</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>jfreechart</artifactId>
+                    <groupId>jfree</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>xercesImpl</artifactId>
+                    <groupId>xerces</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>ssj</artifactId>
+                    <groupId>umontreal.iro.lecuyer.gof</groupId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
     </dependencies>
     <build>
         <plugins>