Newer
Older
<?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>uk.ac.sanger</groupId>
<artifactId>artemis</artifactId>
<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.</description>
<!-- GitHub repo connection -->
<scm>
<connection>scm:https://github.com/sanger-pathogens/Artemis.git</connection>
<url>https://github.com/sanger-pathogens/Artemis</url>
<developerConnection>scm:https://github.com/sanger-pathogens/Artemis.git</developerConnection>
<tag>HEAD</tag>
</scm>
<organization>
<name>Sanger Institute</name>
<url>http://www.sanger.ac.uk/</url>
</organization>
<url>http://sanger-pathogens.github.io/Artemis/</url>
<developers>
<developer>
<id>kp11</id>
<name>Kevin Pepper</name>
<email>artemis-help@sanger.ac.uk</email>
<url>http://www.sanger.ac.uk/science/tools/artemis</url>
<organization>Sanger Institute</organization>
<organizationUrl>http://www.sanger.ac.uk/</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>GB/London</timezone>
</developer>
</developers>
<licenses>
<license>
<name>The GNU General Public License, Version 3, June 2007</name>
<url>https://raw.githubusercontent.com/sanger-pathogens/Artemis/master/LICENSE</url>
</license>
</licenses>
<issueManagement>
<system>Github</system>
<url>https://github.com/sanger-pathogens/Artemis/issues</url>
</issueManagement>
<mailingLists>
<mailingList>
<name>Artemis support email address</name>
<post>artemis-help@sanger.ac.uk</post>
</mailingList>
</mailingLists>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<ignore.test.failures>true</ignore.test.failures>
<version.file>${project.basedir}/etc/versions</version.file>
<!-- Properties passed into Maven on command line -->
<emboss.installation.root>${env.EMBOSS_ROOT}</emboss.installation.root>
<!-- Application names -->
<artemis.application.name>Artemis</artemis.application.name>
<act.application.name>ACT</act.application.name>
<dnaplotter.application.name>Circular-Plot</dnaplotter.application.name>
<bamview.application.name>BamView</bamview.application.name>
<!-- Deployable jar names -->
<artemis.jar.name>artemis.jar</artemis.jar.name>
<act.jar.name>act.jar</act.jar.name>
<bamview.jar.name>bamview.jar</bamview.jar.name>
<dnaplotter.jar.name>dnaplotter.jar</dnaplotter.jar.name>
<!-- Main classes -->
<artemis.main.class>uk.ac.sanger.artemis.components.ArtemisMain</artemis.main.class>
<act.main.class>uk.ac.sanger.artemis.components.ActMain</act.main.class>
<bamview.main.class>uk.ac.sanger.artemis.components.alignment.BamView</bamview.main.class>
<dnaplotter.main.class>uk.ac.sanger.artemis.circular.DNADraw</dnaplotter.main.class>
<!-- Java version-->
<java.source.version>1.8</java.source.version>
<java.target.version>1.8</java.target.version>
<java.javadoc.url>https://docs.oracle.com/javase/8/docs/api/</java.javadoc.url>
<osx.jdk.path>${env.JAVA_HOME}/../..</osx.jdk.path>
<!-- Evosuite properties-->
<targetFolder>src/test/evosuite</targetFolder>
<evosuite.runtime.version>1.0.6</evosuite.runtime.version>
<evosuite.plugin.version>1.0.6</evosuite.plugin.version>
<!-- Assembly folders -->
<windows.assembly.folder>artemis</windows.assembly.folder>
<unix.assembly.folder>artemis</unix.assembly.folder>
<osx.assembly.folder>artemis</osx.assembly.folder>
<!-- Release deliverable folder -->
<release.artifact.folder>${project.build.directory}/release-artifacts</release.artifact.folder>
<windows.release.folder>${release.artifact.folder}/windows-release</windows.release.folder>
<osx.app.folder>${release.artifact.folder}/mac-osx-release</osx.app.folder>
<osx.app.chado.folder>${release.artifact.folder}/mac-osx-chado-release</osx.app.chado.folder>
<unix.release.folder>${release.artifact.folder}/unix-release</unix.release.folder>
<!-- Release file names -->
<unix.release.filename>artemis-unix-release-${project.version}</unix.release.filename>
<windows.release.filename>artemis-windows-release-${project.version}</windows.release.filename>
<osx.release.filename>artemis-macosx-release-${project.version}</osx.release.filename>
<osx.chado.release.filename>artemis-macosx-chado-release-${project.version}</osx.chado.release.filename>
<!-- Mac OS application JVM options -->
<postgres.command.line.arg>-Djdbc.drivers=org.postgresql.Driver</postgres.command.line.arg>
<maxheap.command.line.arg>-mx2g</maxheap.command.line.arg>
<initialheap.command.line.arg>-ms128m</initialheap.command.line.arg>
<noverify.command.line.arg>-noverify</noverify.command.line.arg>
<unixenv.command.line.arg>-Dartemis.environment=UNIX</unixenv.command.line.arg>
<macosx.menuname.command.line.arg>-Dcom.apple.mrj.application.apple.menu.about.name</macosx.menuname.command.line.arg>
<macosx.dock.command.line.arg>-Xdock:name</macosx.dock.command.line.arg>
<chado.command.line.arg>-Dchado="localhost:5432/databasename?username"</chado.command.line.arg>
<ibatis.command.line.arg>-Dibatis</ibatis.command.line.arg>
<sangeroptions.command.line.arg>-Dsanger_options=yes</sangeroptions.command.line.arg>
<j2ssh.command.line.arg>-Dj2ssh</j2ssh.command.line.arg>
<!-- Surefire unit test plugin parameters -->
<surefireArgLine>-Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -Duse_separate_classloader=false -DEMBOSS_ROOT=${emboss.installation.root}</surefireArgLine>
<surefire.num.forks>1</surefire.num.forks>
<!-- Files to exclude from the build, e.g. Mac resource files. -->
<default.file.excludes>**/log4j*.xml META-INF/* **/.DS_Store **/._*</default.file.excludes>
<etc.file.excludes>*.seq *.fasta *.embl *.tab *.crunch *.genbank</etc.file.excludes>
<artemis.icons.path>${project.basedir}/icons</artemis.icons.path>
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
</properties>
<dependencies>
<!-- Start of BATIK Jars -->
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-codec -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-codec</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-dom -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-dom</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-ext -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-ext</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-svggen -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-svggen</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-util -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-util</artifactId>
<version>1.9.1</version>
</dependency>
<!-- End of BATIK Jars -->
<!-- Start of IBATIS jars -->
<!-- https://mvnrepository.com/artifact/com.ibatis/ibatis (local legacy jar) -->
<dependency>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version>
</dependency>
<!-- This is now out of date but is used by the ibatis jar-->
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
<!-- https://mvnrepository.com/artifact/cglib/cglib-nodep -->
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib-nodep</artifactId>
<version>2.2</version>
</dependency>
<!-- This is now out of date - the package name has changed and so updating will mean many changes -->
<!-- https://mvnrepository.com/artifact/log4j/log4j -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<!-- End of IBATIS jars (local) -->
<dependency>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
</dependency>
<!-- Latest commons logging from 2014! -->
<!-- https://mvnrepository.com/artifact/commons-logging/commons-logging -->
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
<!-- End of J2SSH jars (local) -->
<dependency>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
</dependency>
<!-- Very out of date, but using the latest v3 will not compile atm -->
<!-- https://mvnrepository.com/artifact/commons-lang/commons-lang -->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.6</version>
</dependency>
<!-- NOTE: IBatis is no longer supported and very out of date -->
<!-- Using the new postgres driver may cause issues - needs testing -->
<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<!-- Using latest version gives compilation errors! -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>1.6</version>
</dependency>
<!-- Start of Picard jars -->
<!-- https://mvnrepository.com/artifact/com.github.broadinstitute/picard -->
<!-- Latest as of 24th Sept 2018 -->
“kpepper”
committed
<!-- It contains two htsjdk fixes for CRAM index caching and the query mate issue -->
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
“kpepper”
committed
<version>2.18.14</version>
</dependency>
<!-- End of Picard jars -->
<!-- Testing only -->
<!-- https://mvnrepository.com/artifact/junit/junit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.evosuite</groupId>
<artifactId>evosuite-standalone-runtime</artifactId>
<version>${evosuite.runtime.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.25</version>
<scope>test</scope>
</dependency>
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
<!-- Redundant dependencies..... -->
<!-- Latest version as of 2005 -->
<!-- https://mvnrepository.com/artifact/jakarta-regexp/jakarta-regexp -->
<!-- dependency>
<groupId>jakarta-regexp</groupId>
<artifactId>jakarta-regexp</artifactId>
<version>1.4</version>
</dependency-->
<!-- https://mvnrepository.com/artifact/batik/batik-awt-util -->
<!-- dependency>
<groupId>batik</groupId>
<artifactId>batik-awt-util</artifactId>
<version>1.6-1</version>
</dependency-->
<!-- https://mvnrepository.com/artifact/batik/batik-xml -->
<!-- dependency>
<groupId>batik</groupId>
<artifactId>batik-xml</artifactId>
<version>1.6-1</version>
</dependency-->
</dependencies>
<build>
<plugins>
<!-- =================== Evosuite needs at least Maven 3.1 ======================= -->
<plugin>
<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>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.1</version>
</requireMavenVersion>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<!-- ====================== Read signing related properties ======================= -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<id>load-external-properties</id>
<phase>initialize</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<!-- Build will not fail if properties file is not found, but signing will fail -->
<quiet>true</quiet>
<files>
<file>maven.properties</file>
</files>
</configuration>
</execution>
</executions>
</plugin>
<!-- ====================== Install essential old jars into the local Maven repo ======================= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
<executions>
<execution>
<id>install-biojava-jar</id>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>1.6</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/biojava.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-jemalign-jar</id>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/jemAlign.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-j2ssh-core-jar</id>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/j2ssh/j2ssh-core.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/ibatis-2.3.4.726.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
</executions>
</plugin>
<!-- ========= Store release version number to the Artemis splash screen version file ======== -->
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>updating-software-version-number</id>
<phase>initialize</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<echo file="${version.file}">Artemis Release ${project.version}${line.separator}ACT Release ${project.version}${line.separator}DNAPlotter Release ${project.version}${line.separator}BamView ${project.version}</echo>
</target>
</configuration>
</execution>
</executions>
</plugin>
<!-- ==================================== Compile ========================================= -->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>${java.source.version}</source>
<target>${java.target.version}</target>
</configuration>
</plugin>
<!-- ============================== Jar customisation ===================================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>false</addClasspath>
</manifest>
<manifestEntries>
<Permissions>all-permissions</Permissions>
<Codebase>*</Codebase>
</manifestEntries>
</archive>
</configuration>
</plugin>
<!-- ============================== Copy resources to build folder ======================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<executions>
<!-- Copy test data for unit tests -->
<execution>
<id>copy-test-data</id>
<phase>process-test-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.testOutputDirectory}/data</outputDirectory>
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
<resources>
<resource>
<directory>${project.basedir}/test/data</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- Copy etc on to classpath -->
<execution>
<id>copy-property-files</id>
<phase>process-test-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}/etc</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/etc</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- Copy images on to classpath -->
<execution>
<id>copy-image-folder</id>
<phase>process-test-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}/images</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/images</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- Copy non-maven legacy jars to build area for inclusion in assembly -->
<id>copy-old-jars</id>
<phase>process-test-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/lib/**/*.jar</directory>
</resource>
</resources>
</configuration>
<execution>
<id>copy-icons-to-target-folder</id>
<phase>package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<outputDirectory>${project.build.directory}/icons</outputDirectory>
<resources>
<resource>
<directory>${artemis.icons.path}</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============================== Run JUnit tests =============================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.20.1</version>
<configuration>
<skipTests>${skip.tests}</skipTests>
<forkCount>${surefire.num.forks}</forkCount>
<testFailureIgnore>${ignore.test.failures}</testFailureIgnore>
<exclude>${evosuite.exclude.filter}</exclude>
<exclude>**/j2ssh/**</exclude>
<!-- End of Evosuite excludes -->
</excludes>
<!-- Required when running Evosuite tests along with normal tests -->
<properties>
<property>
<name>listener</name>
<value>org.evosuite.runtime.InitializingListener</value>
</property>
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
</configuration>
</plugin>
<!-- ========================= Required for Evosuite test running ========================-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>${targetFolder}</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<!-- =================================== Run Jacoco coverage report ======================================-->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.0</version>
<configuration>
<skip>${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>${project.build.directory}/coverage-report</outputDirectory>
<excludes>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============= Package the code and dependent jars into one executable jar for each applications ========= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>package-nonunix-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${artemis.jar.name}</outputFile>
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-unix-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/unix-jars/${artemis.jar.name}</outputFile>
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-nonunix-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${act.jar.name}</outputFile>
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-unix-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/unix-jars/${act.jar.name}</outputFile>
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-nonunix-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${dnaplotter.jar.name}</outputFile>
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-unix-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/unix-jars/${dnaplotter.jar.name}</outputFile>
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-nonunix-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${bamview.jar.name}</outputFile>
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${bamview.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-unix-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/unix-jars/${bamview.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>