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Commits on Source (4)
No need for get-orig-source target
· 7937c35c
Andreas Tille
authored
May 14, 2018
7937c35c
javahelper
· 8781ff0f
Andreas Tille
authored
May 14, 2018
8781ff0f
Missing Build-Depends + missing packages
· c8e2c2eb
Andreas Tille
authored
May 14, 2018
c8e2c2eb
More existing and not yet existing dependencies (added as TODO in changelog)
· 5acd02d3
Andreas Tille
authored
May 14, 2018
5acd02d3
Show whitespace changes
Inline
Side-by-side
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