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debian/artemis.install
View file @ 9844ab13
......@@ -3,4 +3,3 @@ jar_build/act.jar usr/share/java/
jar_build/bamview.jar usr/share/java/
jar_build/dnaplotter.jar usr/share/java/
debian/desktop/*.desktop usr/share/applications/
images/helix.png usr/share/icons/hicolor/96x96/apps/
debian/artemis.poms 0 → 100644
View file @ 9844ab13
# List of POM files for the package
# Format of this file is:
# <path to pom file> [option]*
# where option can be:
# --ignore: ignore this POM and its artifact if any
# --ignore-pom: don't install the POM. To use on POM files that are created
# temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
# --no-parent: remove the <parent> tag from the POM
# --package=<package>: an alternative package to use when installing this POM
# and its artifact
# --has-package-version: to indicate that the original version of the POM is the same as the upstream part
# of the version for the package.
# --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
# during a clean operation with mh_cleanpom or mh_installpom
# --artifact=<path>: path to the build artifact associated with this POM,
# it will be installed when using the command mh_install. [mh_install]
# --java-lib: install the jar into /usr/share/java to comply with Debian
# packaging guidelines
# --usj-name=<name>: name to use when installing the library in /usr/share/java
# --usj-version=<version>: version to use when installing the library in /usr/share/java
# --no-usj-versionless: don't install the versionless link in /usr/share/java
# --dest-jar=<path>: the destination for the real jar.
# It will be installed with mh_install. [mh_install]
# --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
# Empty by default. [mh_install]
#
pom.xml --has-package-version
debian/control
View file @ 9844ab13
......@@ -4,13 +4,20 @@ Uploaders: Afif Elghraoui <afif@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
default-jdk-headless,
javahelper,
maven-debian-helper,
default-jdk,
maven-debian-helper (>= 2.1)
Build-Depends-Indep: junit4 (>= 4.12),
libbatik-java (>= 1.10),
libcommons-lang3-java,
libcommons-logging-java (>= 1.2),
libcommons-net-java (>= 3.6),
liblog4j1.2-java (>= 1.2.17),
libmaven-antrun-plugin-java (>= 1.8),
libmaven-install-plugin-java (>= 2.5.2),
libmaven-shade-plugin-java (>= 3.1.1),
libpostgresql-jdbc-java (>= 42.2.5),
libslf4j-java (>= 1.7.25),
libmaven-enforcer-plugin-java,
libmaven-install-plugin-java,
libproperties-maven-plugin-java,
libmaven-antrun-plugin-java,
libmaven-resources-plugin-java,
libbuild-helper-maven-plugin-java,
libmaven-jar-plugin-java,
......@@ -19,21 +26,9 @@ Build-Depends: debhelper (>= 12~),
libbiojava-java,
libj2ssh-java,
libibatis-java,
liblog4j1.2-java,
libpostgresql-jdbc-java,
picard-tools,
libhtsjdk-java,
libcommons-net-java,
libcommons-lang3-java,
libbatik-java,
jemboss,
# For tests
ant,
ant-optional,
junit4,
libhamcrest-java,
libjs-jquery,
# To convert gifs to png because gif is not a supported icon format
imagemagick
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/artemis
......
debian/maven.ignoreRules
View file @ 9844ab13
# see https://lists.debian.org/debian-java/2019/01/msg00063.html
org.jacoco jacoco-maven-plugin
org.apache.maven.plugins maven-enforcer-plugin
cglib cglib-nodep * * * *
org.apache.maven.plugins maven-jarsigner-plugin * * * *
org.apache.maven.plugins maven-javadoc-plugin * * * *
org.codehaus.mojo properties-maven-plugin * * * *
org.evosuite evosuite-standalone-runtime * * * *
org.jacoco jacoco-maven-plugin * * * *
org.mockito mockito-core * * * *
debian/maven.properties 0 → 100644
View file @ 9844ab13
# Include here properties to pass to Maven during the build.
# For example:
# maven.test.skip=true
# project.build.sourceEncoding=UTF-8
debian/maven.rules 0 → 100644
View file @ 9844ab13
junit junit jar s/4\..*/4.x/ * *
uk.ac.sanger artemis jar s/.*/debian/ * *
commons-logging s/commons-logging-api/commons-logging/ * s/.*/debian/ * *
log4j log4j * s/1\.2\..*/1.2.x/ * *
org.apache.maven.plugins maven-enforcer-plugin * s/.*/debian/ * *
org.apache.rat apache-rat-plugin * s/.*/debian/ * *
org.codehaus.plexus plexus-container-default * * * *
debian/patches/maven_depencencies.patch deleted 100644 → 0
View file @ edcab6c5
--- a/pom.xml
+++ b/pom.xml
@@ -360,7 +360,6 @@ Artemis is written in Java, and is avail
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
- <version>1.3.1</version>
<executions>
<execution>
<id>enforce-maven-3</id>
@@ -499,7 +498,6 @@ Artemis is written in Java, and is avail
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
- <version>3.0.2</version>
<executions>
<!-- Copy etc on to classpath -->
<execution>
@@ -554,7 +552,6 @@ Artemis is written in Java, and is avail
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
- <version>3.1.0</version>
<configuration>
<archive>
<manifest>
@@ -616,55 +613,12 @@ Artemis is written in Java, and is avail
</configuration>
</plugin>
- <!-- =================================== Run Jacoco coverage report ======================================-->
-
- <plugin>
- <groupId>org.jacoco</groupId>
- <artifactId>jacoco-maven-plugin</artifactId>
- <version>0.8.2</version>
- <configuration>
- <skip>${skip.coverage.reporting}</skip>
- </configuration>
- <executions>
- <execution>
- <id>pre-unit-test</id>
- <goals>
- <goal>prepare-agent</goal>
- </goals>
- <configuration>
- <output>file</output>
- <!-- Sets the path to the file which contains the execution data. -->
- <destFile>${project.build.directory}/jacoco-ut.exec</destFile>
- <!-- Sets the name of the property containing the settings for JaCoCo
- runtime agent. -->
- <propertyName>surefireArgLine</propertyName>
- </configuration>
- </execution>
- <!-- Ensures that the code coverage report for unit tests is created after
- unit tests have been run. -->
- <execution>
- <id>post-unit-test</id>
- <phase>test</phase>
- <goals>
- <goal>report</goal>
- </goals>
- <configuration>
- <dataFile>${project.build.directory}/jacoco-ut.exec</dataFile>
- <outputDirectory>${project.build.directory}/coverage-report</outputDirectory>
- <excludes>
- <exclude>org/**</exclude>
- </excludes>
- </configuration>
- </execution>
- </executions>
- </plugin>
<!-- ============= Package the code and dependent jars into one executable jar for each applications ========= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
- <version>3.1.0</version>
<executions>
<execution>
<id>package-win-artemis-jar</id>
@@ -1005,66 +959,12 @@ Artemis is written in Java, and is avail
</plugin>
- <!-- ============================= Sign executable jar files ============================ -->
-
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jarsigner-plugin</artifactId>
- <version>1.4</version>
- <executions>
- <execution>
- <id>sign-win-jars</id>
- <phase>package</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- <configuration>
- <skip>${jarsigner.skip}</skip>
- <verbose>false</verbose>
- <processMainArtifact>false</processMainArtifact>
- <processAttachedArtifacts>false</processAttachedArtifacts>
- <archiveDirectory>target/win-jars</archiveDirectory>
- <keystore>${signer-keystore-path}</keystore>
- <storetype>${signer-keystore-type}</storetype>
- <alias>${signer-keystore-alias}</alias>
- <storepass>${signer-keystore-password}</storepass>
- <keypass>${signer-keystore-password}</keypass>
- <removeExistingSignatures>true</removeExistingSignatures>
- <tsa>http://timestamp.comodoca.com/rfc3161</tsa>
- </configuration>
- </execution>
- <execution>
- <id>sign-default-jars</id>
- <phase>package</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- <configuration>
- <skip>${jarsigner.skip}</skip>
- <verbose>false</verbose>
- <processMainArtifact>false</processMainArtifact>
- <processAttachedArtifacts>false</processAttachedArtifacts>
- <archiveDirectory>target/jars</archiveDirectory>
- <keystore>${signer-keystore-path}</keystore>
- <storetype>${signer-keystore-type}</storetype>
- <alias>${signer-keystore-alias}</alias>
- <storepass>${signer-keystore-password}</storepass>
- <keypass>${signer-keystore-password}</keypass>
- <removeExistingSignatures>true</removeExistingSignatures>
- <tsa>http://timestamp.comodoca.com/rfc3161</tsa>
- </configuration>
- </execution>
- </executions>
-
- </plugin>
-
<!-- ========================== Create release zips ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
- <version>3.1.0</version>
<executions>
<execution>
<id>create-unix-release</id>
@@ -1350,10 +1250,6 @@ Artemis is written in Java, and is avail
<properties>
<skip.tests>false</skip.tests>
<evosuite.exclude.filter></evosuite.exclude.filter>
- <jarsigner.skip>false</jarsigner.skip>
- <skip.artifact.creation>false</skip.artifact.creation>
- <skip.coverage.reporting>false</skip.coverage.reporting>
- <skip.javadoc>false</skip.javadoc>
<build.profile.id>release</build.profile.id>
</properties>
debian/patches/series
View file @ 9844ab13
......@@ -2,4 +2,3 @@ samreader.patch
use-lang3.patch
#build-test.patch
#disable-tests.patch
maven_depencencies.patch
debian/rules
View file @ 9844ab13
......@@ -35,13 +35,17 @@ CLASSPATH += /usr/share/EMBOSS/jemboss/lib/jemboss.jar \
export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))
%:
dh $@ --with javahelper --buildsystem=maven
dh $@
__override_dh_auto_build:
dh_auto_build -- jar
sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \
debian/artemis.manifest
convert images/helix.gif -resize 96x96\! images/helix.png
override_dh_install:
dh_install
mkdir -p debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/
convert src/main/resources/images/helix.gif -resize 96x96\! debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/helix.png
__override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
......