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Initial upload.
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jj-umn committed Jun 1, 2015
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340 changes: 340 additions & 0 deletions LICENSE
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8 changes: 6 additions & 2 deletions README.md
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# mzToSQLite
Convert proteomics data files into a SQLite database
# mztosqlite
Convert proteomics data files into a SQLite database

Extract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.
The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin.

51 changes: 51 additions & 0 deletions dependency-reduced-pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.umn.msi.gx</groupId>
<artifactId>mzToSQLite</artifactId>
<version>1.0-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer>
<mainClass>edu.umn.msi.gx.mztosqlite.MzToSQLite</mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>tmate</id>
<url>http://maven.tmatesoft.com/content/repositories/releases</url>
</repository>
</repositories>
<properties>
<java.mail.version>1.4.4</java.mail.version>
<pride.utilities.version>0.1.21</pride.utilities.version>
<jmzidentml.version>1.1.4-SNAPSHOT</jmzidentml.version>
<assembly.dir>${name}-${version}</assembly.dir>
<pride.jaxb.version>1.0.8</pride.jaxb.version>
<apache.commons.net.version>3.0.1</apache.commons.net.version>
<apache.http.client>4.2.1</apache.http.client>
<maven.compiler.target>1.7</maven.compiler.target>
<java.help.version>2.0.02</java.help.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.webstart.version>1.5.0</java.webstart.version>
<maven.compiler.source>1.7</maven.compiler.source>
</properties>
</project>

18 changes: 18 additions & 0 deletions nb-configuration.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project-shared-configuration>
<!--
This file contains additional configuration written by modules in the NetBeans IDE.
The configuration is intended to be shared among all the users of project and
therefore it is assumed to be part of version control checkout.
Without this configuration present, some functionality in the IDE may be limited or fail altogether.
-->
<properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
<!--
Properties that influence various parts of the IDE, especially code formatting and the like.
You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
That way multiple projects can share the same settings (useful for formatting rules for example).
Any value defined here will override the pom.xml file value but is only applicable to the current project.
-->
<netbeans.hint.jdkPlatform>JDK_1.7</netbeans.hint.jdkPlatform>
</properties>
</project-shared-configuration>
46 changes: 46 additions & 0 deletions nbactions.xml
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<?xml version="1.0" encoding="UTF-8"?>
<actions>
<action>
<actionName>run</actionName>
<packagings>
<packaging>jar</packaging>
</packagings>
<goals>
<goal>process-classes</goal>
<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/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>
<action>
<actionName>debug</actionName>
<packagings>
<packaging>jar</packaging>
</packagings>
<goals>
<goal>process-classes</goal>
<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/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>
</action>
<action>
<actionName>profile</actionName>
<packagings>
<packaging>jar</packaging>
</packagings>
<goals>
<goal>process-classes</goal>
<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/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>
</actions>
180 changes: 180 additions & 0 deletions pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.umn.msi.gx</groupId>
<artifactId>mzToSQLite</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<jmzidentml.version>1.1.4-SNAPSHOT</jmzidentml.version>
<pride.jaxb.version>1.0.8</pride.jaxb.version>
<pride.utilities.version>0.1.21</pride.utilities.version>
<apache.commons.net.version>3.0.1</apache.commons.net.version>
<apache.http.client>4.2.1</apache.http.client>
<java.mail.version>1.4.4</java.mail.version>
<java.webstart.version>1.5.0</java.webstart.version>
<java.help.version>2.0.02</java.help.version>
<assembly.dir>${name}-${version}</assembly.dir>
</properties>
<repositories>
<repository>
<id>tmate</id>
<url>http://maven.tmatesoft.com/content/repositories/releases</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>1.6.8</version>
<exclusions>
<exclusion>
<artifactId>xxindex</artifactId>
<groupId>psidev.psi.tools</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>1.1.10-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.mzgraph</groupId>
<artifactId>pride-mzgraph-browser</artifactId>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>jmzreader</artifactId>
<version>1.2.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>pkl-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>dta-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>ms2-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mgf-parser</artifactId>
<version>1.2.4</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzxml-parser</artifactId>
<version>1.3.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzdata-parser</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzml-wrapper</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>pride-wrapper</artifactId>
<version>1.2.0</version>
</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>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>edu.umn.msi.gx.mztosqlite.MzToSQLite</mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
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