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debian/changelog
View file @ 5acd02d3
snpeff (4.3t+dfsg-1) unstable; urgency=low
* Initial release (Closes: #<bug>)
TODO:
apfloat 1.6.3:
https://github.com/mtommila/apfloat
http://www.apfloat.org/apfloat_java/maven.html
charts4j 1.3:
https://mvnrepository.com/artifact/com.googlecode.charts4j/charts4j/1.3
com.typesafe.akka:akka-actor 2.0.1
distlib 0.9.1:
https://sourceforge.net/projects/statdistlib/?source=navbar
-- Andreas Tille <tille@debian.org> Mon, 14 May 2018 22:07:57 +0200
debian/control
View file @ 5acd02d3
......@@ -4,8 +4,21 @@ Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
javahelper,
default-jdk,
maven-debian-helper,
libmaven-assembly-plugin-java,
libtrove-java,
liblog4j2-java
liblog4j2-java,
libhtsjdk-java,
libbiojava4-java,
junit4,
libcommons-codec-java,
libcommons-io-java,
libcommons-cli-java,
libcommons-math3-java,
libcommons-cli-java-doc,
libfreemarker-java
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/snpeff
Vcs-Git: https://salsa.debian.org/med-team/snpeff.git
......
debian/rules
View file @ 5acd02d3
......@@ -2,9 +2,7 @@
# DH_VERBOSE := 1
%:
dh $@
export JAVA_HOME=/usr/lib/jvm/default-java
get-orig-source:
# Need to write a script fetching an export from
# https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/
%:
dh $@ --with javahelper
pom.xml
View file @ 5acd02d3
<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">
<?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>org.snpeff</groupId>
<artifactId>SnpEff</artifactId>
<packaging>jar</packaging>
<version>4.3</version>
<packaging>jar</packaging><properties>
<debian.hasPackageVersion/>
<debian.mavenRules>org.snpeff SnpEff jar s/.*/debian/ * *</debian.mavenRules>
<debian.originalVersion>4.3</debian.originalVersion>
<debian.package>libsnpeff-java</debian.package>
</properties>
<name>Snp Effect</name>
<description>Variant annotation and effect prediction package.</description>
<url>http://snpeff.sourceforge.net/</url>
......@@ -27,72 +38,46 @@
<email>pcingola@users.sourceforge.net</email>
</developer>
</developers>
<dependencies>
<dependency>
<groupId>org.apfloat</groupId>
<artifactId>apfloat</artifactId>
<version>1.6.3</version>
</dependency>
<dependency>
<groupId>com.googlecode.charts4j</groupId>
<artifactId>charts4j</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-actor</artifactId>
<version>2.0.1</version>
<version>debian</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.4</version>
<version>4.x</version>
</dependency>
<dependency>
<groupId>net.sf.trove4j</groupId>
<artifactId>trove4j</artifactId>
<version>3.0.2</version>
<version>2.x</version>
</dependency>
<dependency>
<groupId>org.freemarker</groupId>
<artifactId>freemarker</artifactId>
<version>2.3.19</version>
</dependency>
<dependency>
<groupId>distlib</groupId>
<artifactId>distlib</artifactId>
<version>0.9.1</version>
</dependency>
<dependency>
<groupId>samtools</groupId>
<artifactId>samtools</artifactId>
<version>1.107</version>
<version>debian</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.2</version>
<version>debian</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
<version>debian</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.10</version>
<version>debian</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.15</version>
<version>1.2.x</version>
<exclusions>
<exclusion>
<groupId>com.sun.jdmk</groupId>
......@@ -104,18 +89,7 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0.7</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-structure</artifactId>
<version>3.0.7</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>central</id>
......@@ -142,7 +116,6 @@
<url>http://repo.typesafe.com/typesafe/releases/</url>
</repository>
</repositories>
<build>
<plugins>
<plugin>
......@@ -165,30 +138,6 @@
<encoding>ISO-8859-1</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.snpeff.SnpEff</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.8.1</version>
<configuration>
<encoding>ISO-8859-1</encoding>
</configuration>
</plugin>
</plugins>
</build>
<version>4.3</version>
</project>
\ No newline at end of file