[med-svn] [Git][med-team/snpeff][master] 10 commits: routine-update: Standards-Version: 4.5.0
Andreas Tille
gitlab at salsa.debian.org
Wed Apr 22 14:23:23 BST 2020
Andreas Tille pushed to branch master at Debian Med / snpeff
Commits:
0eddec15 by Andreas Tille at 2020-04-22T15:04:11+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
58c23805 by Andreas Tille at 2020-04-22T15:04:11+02:00
routine-update: debhelper-compat 12
- - - - -
ece433bb by Andreas Tille at 2020-04-22T15:04:18+02:00
routine-update: Secure URI in copyright format
- - - - -
ecffd922 by Andreas Tille at 2020-04-22T15:04:18+02:00
R-U: Trailing whitespace in debian/control
- - - - -
52438ab9 by Andreas Tille at 2020-04-22T15:04:18+02:00
routine-update: Add salsa-ci file
- - - - -
b8687728 by Andreas Tille at 2020-04-22T15:04:18+02:00
routine-update: Rules-Requires-Root: no
- - - - -
fbccf858 by Andreas Tille at 2020-04-22T15:04:49+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
c800aebe by Andreas Tille at 2020-04-22T15:06:20+02:00
Cleanup d/changelog
- - - - -
62c8599c by Andreas Tille at 2020-04-22T15:06:58+02:00
Revert unintended change of upstream source
- - - - -
37ff883a by Andreas Tille at 2020-04-22T15:22:55+02:00
Add patch I've found on my hard disk - I forgot the purpose. :-(
- - - - -
9 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/pom_xml.patch
- + debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata
- pom.xml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-snpeff (4.3t+dfsg-1) unstable; urgency=low
+snpeff (4.3t+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
TODO:
@@ -11,4 +11,4 @@ snpeff (4.3t+dfsg-1) unstable; urgency=low
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
+ -- Andreas Tille <tille at debian.org> Wed, 22 Apr 2020 15:04:51 +0200
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
javahelper,
default-jdk,
default-jdk-doc,
@@ -28,10 +28,11 @@ Build-Depends: debhelper (>= 11~),
libfreemarker-java-doc,
liblog4j1.2-java-doc,
libtrove-java-doc
-Standards-Version: 4.1.4
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/snpeff
Vcs-Git: https://salsa.debian.org/med-team/snpeff.git
Homepage: http://snpeff.sourceforge.net/
+Rules-Requires-Root: no
Package: snpeff
Architecture: all
@@ -40,7 +41,7 @@ Depends: ${shlibs:Depends},
Description: genetic variant annotation and effect prediction toolbox
SnpEff is a variant annotation and effect prediction tool. It annotates
and predicts the effects of variants on genes (such as amino acid
- changes).
+ changes).
.
The inputs are predicted variants (SNPs, insertions, deletions and
MNPs). The input file is usually obtained as a result of a sequencing
@@ -49,7 +50,7 @@ Description: genetic variant annotation and effect prediction toolbox
SnpEff analyzes the input variants. It annotates the variants and
calculates the effects they produce on known genes (e.g. amino acid
changes). A list of effects and annotations that SnpEff can calculate
- can be found here.
+ can be found here.
Package: libsnpeff-java
Architecture: all
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola at users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
=====================================
debian/patches/pom_xml.patch
=====================================
@@ -0,0 +1,339 @@
+Author: Andreas Tille
+FIXME: I've found this on my hard disk some time ago - no idea what I was approaching
+
+--- 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
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+pom_xml.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/pcingola/SnpEff/issues
+Bug-Submit: https://github.com/pcingola/SnpEff/issues/new
Reference:
Author: >
Pablo Cingolani and Adrian Platts and Le Lily Wang and Melissa Coon
@@ -23,3 +25,5 @@ Registry:
Entry: snpeff
- Name: conda:bioconda
Entry: snpeff
+Repository: https://github.com/pcingola/SnpEff.git
+Repository-Browse: https://github.com/pcingola/SnpEff
=====================================
pom.xml
=====================================
@@ -1,143 +1,194 @@
-<?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>
- <!--
+<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>
+ <!--
<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>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
+ <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>
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/02ca4cc1acb302e2d8e9cea38701943bfeba4357...37ff883afe90e52c6c838c99922bc59c89f90f6b
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/02ca4cc1acb302e2d8e9cea38701943bfeba4357...37ff883afe90e52c6c838c99922bc59c89f90f6b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200422/83183bce/attachment-0001.html>
More information about the debian-med-commit
mailing list