[med-svn] [Git][med-team/snpeff][master] 4 commits: No need for get-orig-source target
Andreas Tille
gitlab at salsa.debian.org
Mon May 14 22:29:14 BST 2018
Andreas Tille pushed to branch master at Debian Med / snpeff
Commits:
7937c35c by Andreas Tille at 2018-05-14T22:40:36+02:00
No need for get-orig-source target
- - - - -
8781ff0f by Andreas Tille at 2018-05-14T22:55:16+02:00
javahelper
- - - - -
c8e2c2eb by Andreas Tille at 2018-05-14T23:14:35+02:00
Missing Build-Depends + missing packages
- - - - -
5acd02d3 by Andreas Tille at 2018-05-14T23:28:20+02:00
More existing and not yet existing dependencies (added as TODO in changelog)
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/rules
- pom.xml
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,14 @@
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 at debian.org> Mon, 14 May 2018 22:07:57 +0200
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -4,8 +4,21 @@ Uploaders: Andreas Tille <tille at 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
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -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
=====================================
--- a/pom.xml
+++ b/pom.xml
@@ -1,194 +1,143 @@
-<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>
- <name>Snp Effect</name>
- <description>Variant annotation and effect prediction package.</description>
- <url>http://snpeff.sourceforge.net/</url>
- <licenses>
- <license>
- <name>GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0</name>
- <url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
- <distribution>repo</distribution>
- </license>
- </licenses>
- <!--
+<?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>
+ <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>
+ <licenses>
+ <license>
+ <name>GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0</name>
+ <url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+ <!--
<scm>
<url>https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/</url>
<connection>https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/</connection>
</scm>
-->
- <developers>
- <developer>
- <id>pcingola</id>
- <name>Pablo Cingolani</name>
- <email>pcingola at 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>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.4</version>
- </dependency>
- <dependency>
- <groupId>net.sf.trove4j</groupId>
- <artifactId>trove4j</artifactId>
- <version>3.0.2</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>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>commons-math3</artifactId>
- <version>3.2</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>2.4</version>
- </dependency>
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>1.10</version>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>1.2.15</version>
- <exclusions>
- <exclusion>
- <groupId>com.sun.jdmk</groupId>
- <artifactId>jmxtools</artifactId>
- </exclusion>
- <exclusion>
- <groupId>com.sun.jmx</groupId>
- <artifactId>jmxri</artifactId>
- </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>
- <name>Central Repository</name>
- <url>http://repo.maven.apache.org/maven2</url>
- <layout>default</layout>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- </repository>
- <repository>
- <id>hadoop-bam</id>
- <name>Hadoop-BAM</name>
- <url>http://hadoop-bam.sourceforge.net/maven/</url>
- </repository>
- <repository>
- <id>ncimvn-public</id>
- <name>Public NIH repository</name>
- <url>https://ncimvn.nci.nih.gov/nexus/content/groups/public/</url>
- </repository>
- <repository>
- <id>typesafe</id>
- <name>Typesafe Repository</name>
- <url>http://repo.typesafe.com/typesafe/releases/</url>
- </repository>
- </repositories>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.3.2</version>
- <configuration>
- <source>1.8</source>
- <target>1.8</target>
- <encoding>ISO-8859-1</encoding>
- <showDeprecation>true</showDeprecation>
- <showWarnings>true</showWarnings>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-resources-plugin</artifactId>
- <version>2.4.3</version>
- <configuration>
- <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>
+ <developers>
+ <developer>
+ <id>pcingola</id>
+ <name>Pablo Cingolani</name>
+ <email>pcingola at users.sourceforge.net</email>
+ </developer>
+ </developers>
+ <dependencies>
+ <dependency>
+ <groupId>commons-cli</groupId>
+ <artifactId>commons-cli</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.x</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.trove4j</groupId>
+ <artifactId>trove4j</artifactId>
+ <version>2.x</version>
+ </dependency>
+ <dependency>
+ <groupId>org.freemarker</groupId>
+ <artifactId>freemarker</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math3</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>debian</version>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>1.2.x</version>
+ <exclusions>
+ <exclusion>
+ <groupId>com.sun.jdmk</groupId>
+ <artifactId>jmxtools</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>com.sun.jmx</groupId>
+ <artifactId>jmxri</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <id>central</id>
+ <name>Central Repository</name>
+ <url>http://repo.maven.apache.org/maven2</url>
+ <layout>default</layout>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ </repository>
+ <repository>
+ <id>hadoop-bam</id>
+ <name>Hadoop-BAM</name>
+ <url>http://hadoop-bam.sourceforge.net/maven/</url>
+ </repository>
+ <repository>
+ <id>ncimvn-public</id>
+ <name>Public NIH repository</name>
+ <url>https://ncimvn.nci.nih.gov/nexus/content/groups/public/</url>
+ </repository>
+ <repository>
+ <id>typesafe</id>
+ <name>Typesafe Repository</name>
+ <url>http://repo.typesafe.com/typesafe/releases/</url>
+ </repository>
+ </repositories>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
+ <configuration>
+ <source>1.8</source>
+ <target>1.8</target>
+ <encoding>ISO-8859-1</encoding>
+ <showDeprecation>true</showDeprecation>
+ <showWarnings>true</showWarnings>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.4.3</version>
+ <configuration>
+ <encoding>ISO-8859-1</encoding>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/snpeff/compare/da15a77f2d8cb36e61ae462f8d425dcd78df830c...5acd02d3bf9abf117a091ae23160937eabfaa257
---
View it on GitLab: https://salsa.debian.org/med-team/snpeff/compare/da15a77f2d8cb36e61ae462f8d425dcd78df830c...5acd02d3bf9abf117a091ae23160937eabfaa257
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