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Description: Adding missing dependencies to the various pom.xml files
Author: Pierre Gruet <pgt@debian.org>
Forwarded: https://github.com/CampagneLaboratory/goby3/issues/6
Last-Update: 2020-10-31
--- a/goby-io/pom.xml
+++ b/goby-io/pom.xml
@@ -433,6 +433,24 @@
<version>0.9-7</version>
</dependency>
+ <dependency>
+ <groupId>com.martiansoftware</groupId>
+ <artifactId>jsap</artifactId>
+ <version>debian</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>debian</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>debian</version>
+ </dependency>
+
</dependencies>
</project>
--- a/goby-distribution/pom.xml
+++ b/goby-distribution/pom.xml
@@ -140,6 +140,11 @@
<version>2.6</version>
</dependency>
<dependency>
+ <groupId>commons-cli</groupId>
+ <artifactId>commons-cli</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.1</version>
@@ -193,7 +198,9 @@
<dependency>
<groupId>org.rosuda.REngine</groupId>
<artifactId>REngine</artifactId>
- <version>2.1.0</version>
+ <version>debian</version>
+ <scope>system</scope>
+ <systemPath>/usr/lib/R/site-library/rJava/jri/JRI.jar</systemPath>
</dependency>
<dependency>
<groupId>com.github.lucarosellini.rJava</groupId>
@@ -240,9 +247,7 @@
<dependency>
<groupId>edu.rit.pj</groupId>
<artifactId>pj</artifactId>
- <version>1.0</version>
- <scope>system</scope>
- <systemPath>${basedir}/../lib/pj20091226.jar</systemPath>
+ <version>debian</version>
</dependency>
<dependency>
<groupId>edu.mssm.crover</groupId>
@@ -339,10 +344,18 @@
</dependency>
<dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>debian</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>2.6.0</version>
- <scope>test</scope>
+ <scope>system</scope>
+ <systemPath>/usr/share/java/picard.jar</systemPath>
</dependency>
<dependency>
<groupId>it.unimi.dsi</groupId>
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