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Some comments and possible fix in pom file
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@josemduarte
josemduarte committed Sep 23, 2016
1 parent 1366686 commit 88fd080
Showing 1 changed file with 116 additions and 116 deletions.
232 changes: 116 additions & 116 deletions eppic-cli/pom.xml
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Original file line number Diff line number Diff line change
@@ -1,67 +1,67 @@
<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>
<parent>
<groupId>org.eppic-web</groupId>
<artifactId>eppic</artifactId>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>eppic-cli</artifactId>
<parent>
<groupId>org.eppic-web</groupId>
<artifactId>eppic</artifactId>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>eppic-cli</artifactId>

<properties>
<biojava.version>4.2.3</biojava.version>
</properties>

<repositories>
<!-- for uniprot japi -->
<repository>
<id>ebi-repo</id>
<name>ebi-repo</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
</repository>
<id>ebi-repo</id>
<name>ebi-repo</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
</repository>
</repositories>


<dependencies>
<dependency>
<groupId>com.github.spullara.mustache.java</groupId>
<artifactId>compiler</artifactId>
<version>0.8.18</version>
</dependency>
<dependency>

<dependency>
<groupId>org.eppic-web</groupId>
<artifactId>eppic-model</artifactId>
<version>${project.version}</version>
<scope>compile</scope>
</dependency>

<dependency>
<groupId>java3d</groupId>
<artifactId>vecmath</artifactId>
<version>1.3.1</version>
</dependency>

<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>${biojava.version}</version>
<artifactId>biojava-core</artifactId>
<version>${biojava.version}</version>
</dependency>

<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure-gui</artifactId>
<version>${biojava.version}</version>
<artifactId>biojava-structure-gui</artifactId>
<version>${biojava.version}</version>
</dependency>

<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>${biojava.version}</version>
<artifactId>biojava-structure</artifactId>
<version>${biojava.version}</version>
</dependency>

<!-- junit -->

<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
Expand Down Expand Up @@ -97,7 +97,7 @@
<version>${log4j.version}</version>
<scope>compile</scope>
</dependency>

<!-- jgrapht for assembly package -->
<dependency>
<groupId>org.jgrapht</groupId>
Expand All @@ -123,7 +123,7 @@
<artifactId>java-getopt</artifactId>
<version>1.0.13</version>
</dependency>

<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
Expand All @@ -132,70 +132,69 @@

<!-- uniprot -->
<dependency>
<groupId>uk.ac.ebi.uniprot</groupId>
<artifactId>japi</artifactId>
<version>1.0.8</version>
</dependency>


<groupId>uk.ac.ebi.uniprot</groupId>
<artifactId>japi</artifactId>
<version>1.0.8</version>
<exclusions>
<!-- This should fix the problem of multiple bindings (warning at startup). But it doesn't because something
in the UniProt japi calls a logback function at runtime and then the JVM crashes with a NoClassDefFoundError.
I've submitted a bug report to the UniProt people - JD 2016-09-23 -->
<!--
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
-->
</exclusions>
</dependency>


<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.14</version>
</dependency>


</dependencies>

<build>

<!-- one possible way to include sources in jar for gwt compiler to be able to work in eppic-wui -->
<!--
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*.java</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<includes>
<include>**/*.*xml</include>
<include>**/*.*properties</include>
</includes>
</resource>
</resources>
-->


<!-- one possible way to include sources in jar for gwt compiler to be
able to work in eppic-wui -->
<!-- <resources> <resource> <directory>src/main/java</directory> <includes>
<include>**/*.java</include> </includes> </resource> <resource> <directory>src/main/resources</directory>
<includes> <include>**/*.*xml</include> <include>**/*.*properties</include>
</includes> </resource> </resources> -->

<plugins>
<!-- jar plugin to add eppic's main class, so that the jar is executable -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>eppic.Main</mainClass>
</manifest>
</archive>
</configuration>
</manifest>
</archive>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>


<!-- the shade plugin to repack all jars into one uber-jar -->

<!-- the shade plugin to repack all jars into one uber-jar -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
Expand All @@ -206,57 +205,58 @@
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<!-- solution to the signature repackaging problem is this filter: exclude the signatures! -->
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<filters>
<filter>
<!-- solution to the signature repackaging problem is this filter:
exclude the signatures! -->
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<configuration>
<finalName>uber-${project.artifactId}-${project.version}</finalName>
</configuration>
</plugin>

<!-- assembly plugin for final packaging -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<descriptor>src/assembly/bin.xml</descriptor>
<finalName>${project.artifactId}-${project.version}</finalName>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<descriptor>src/assembly/bin.xml</descriptor>
<finalName>${project.artifactId}-${project.version}</finalName>

<archiverConfig>
<fileMode>0644</fileMode>
<directoryMode>0755</directoryMode>
<defaultDirectoryMode>0755</defaultDirectoryMode>
</archiverConfig>
</configuration>
<executions>
<execution>

<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>

</configuration>

<executions>
<execution>

<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

</plugins>
</build>




</project>

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