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Update some build plugin versions in POMs (to fix build errors and so…
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…me warnings in the latest IntelliJ)
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@harmjanwestra
harmjanwestra committed Jul 25, 2019
1 parent 33903c6 commit f10c6cc
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Showing 19 changed files with 716 additions and 690 deletions.
4 changes: 3 additions & 1 deletion BinaryMetaAnalyzer/pom.xml
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<parent>
<groupId>nl.systemsgenetics</groupId>
<artifactId>systemsgenetics</artifactId>
<version>1.0.3-SNAPSHOT</version>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>BinaryMetaAnalyzer</artifactId>
<version>1.0.16-SNAPSHOT</version>
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<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
Expand All @@ -76,6 +77,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
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6 changes: 3 additions & 3 deletions DEPICT2/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>nl.systemsgenetics</groupId>
<artifactId>systemsgenetics</artifactId>
<version>1.0.3-SNAPSHOT</version>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>DEPICT2</artifactId>
<version>2.0.17-SNAPSHOT</version>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.1</version>
<version>3.1.2</version>
<!-- The configuration of the plugin -->
<configuration>
<!-- Configuration of the archiver -->
Expand All @@ -71,7 +71,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
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198 changes: 100 additions & 98 deletions Decon2/Decon-eQTL/pom.xml
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@@ -1,99 +1,101 @@
<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>Decon-eQTL</groupId>
<artifactId>Decon-eQTL</artifactId>
<packaging>jar</packaging>
<version>v1.3.0</version>
<name>Decon-eQTL</name>
<description>Decon-eQTL is part of Decon2, a statistical framework for estimating cell counts using molecular profiling such as expression or methylation data from heterogeneous samples (Decon-cell) and consecutive deconvolution of expression quantitative trait loci (Decon-eQTL) into each cell subpopulation.</description>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>main.java.decon_eQTL.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<id>default-jar</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
</plugins>
</build>
<url>https://github.com/molgenis/systemsgenetics/tree/master/Decon2/Decon-eQTL</url>
<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.7</version>
</dependency>
<dependency>
<groupId>net.sf.jsci</groupId>
<artifactId>jsci</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.5</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
</dependencies>
<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>Decon-eQTL</groupId>
<artifactId>Decon-eQTL</artifactId>
<packaging>jar</packaging>
<version>v1.3.0</version>
<name>Decon-eQTL</name>
<description>Decon-eQTL is part of Decon2, a statistical framework for estimating cell counts using molecular profiling such as expression or methylation data from heterogeneous samples (Decon-cell) and consecutive deconvolution of expression quantitative trait loci (Decon-eQTL) into each cell subpopulation.</description>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>main.java.decon_eQTL.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.2</version>
<executions>
<execution>
<id>default-jar</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
</plugins>
</build>
<url>https://github.com/molgenis/systemsgenetics/tree/master/Decon2/Decon-eQTL</url>
<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.7</version>
</dependency>
<dependency>
<groupId>net.sf.jsci</groupId>
<artifactId>jsci</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.5</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
</dependencies>
</project>
5 changes: 3 additions & 2 deletions FunctionEnrichmentOfTransQtls/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>nl.systemsgenetics</groupId>
<artifactId>systemsgenetics</artifactId>
<version>1.0.3-SNAPSHOT</version>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>FunctionEnrichmentOfTransQtls</artifactId>
<packaging>jar</packaging>
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<!-- The configuration of maven-jar-plugin -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
Expand All @@ -77,7 +78,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
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2 changes: 1 addition & 1 deletion GadoCommandline/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>nl.systemsgenetics</groupId>
<artifactId>systemsgenetics</artifactId>
<version>1.0.3-SNAPSHOT</version>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>GadoCommandline</artifactId>
<version>1.0.1</version>
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