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First commit of Maven build changes
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@kpepper
kpepper committed Mar 21, 2018
1 parent 8951e2b commit 6152b5f
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60 changes: 42 additions & 18 deletions .classpath
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@@ -1,31 +1,55 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="ant-build|cobertura-lib|coverage-report|data|docs|evosuite-dependencies|evosuite-libs|evosuite-tests|jacoco-lib|lib|evosuite-tests/" including="uk/**" kind="src" output="eclipse-classes" path="test"/>
<classpathentry including="uk/**" kind="src" output="eclipse-classes" path="test/evosuite-tests"/>
<classpathentry excluding="main/" kind="src" path="ant-build/src"/>
<classpathentry excluding="ant-build/classes/|ant-build/src/|docs|test|test/evosuite-tests/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="org/|uk/" kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry excluding="ant-build|cobertura-lib|coverage-report|data|docs|evosuite-dependencies|evosuite-libs|evosuite-tests|jacoco-lib|lib" including="uk/**" kind="src" output="eclipse-classes" path="test"/>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path="src/assembly"/>
<classpathentry kind="src" output="target/test-classes" path="src/test/evosuite">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path="src/site"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="lib" path="lib/jemAlign.jar"/>
<classpathentry kind="lib" path="lib/jakarta-regexp-1.2.jar"/>
<classpathentry kind="lib" path="lib/biojava.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/j2ssh-core.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/j2ssh-artemis-plugin.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/commons-logging.jar"/>
<classpathentry kind="lib" path="lib/ibatis/ibatis-2.3.4.726.jar"/>
<classpathentry kind="lib" path="lib/ibatis/log4j-1.2.14.jar"/>
<classpathentry kind="lib" path="lib/postgresql-8.4-701.jdbc3.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-awt-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-codec.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-dom.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-ext.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-svggen.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>
<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
<classpathentry kind="lib" path="test/lib/junit-4.11.jar"/>
<classpathentry kind="lib" path="/Users/kp11/workspace/applications/Artemis/eclipse-classes"/>
<classpathentry kind="lib" path="test/evosuite-lib/evosuite-1.0.5.jar"/>
<classpathentry kind="lib" path="lib/commons-net-3.6.jar"/>
<classpathentry kind="lib" path="lib/picard/picard.jar"/>
<classpathentry kind="output" path="eclipse-classes"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
7 changes: 5 additions & 2 deletions .gitignore
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@@ -1,7 +1,5 @@
*.class
.settings
ant-build
test/ant-build
**/.DS_Store
**/*.log
test/coverage-report
Expand All @@ -10,3 +8,8 @@ tar_build
artemis_compiled.tar
/eclipse-classes/
/test-kjp/
.scaffolding*
/target/
**/.scaffolding_list.tmp
dependency-reduced-pom.xml
maven.properties
6 changes: 6 additions & 0 deletions .project
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Expand Up @@ -10,8 +10,14 @@
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
2 changes: 0 additions & 2 deletions META-INF/MANIFEST.MF
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18 changes: 2 additions & 16 deletions act
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Expand Up @@ -137,22 +137,8 @@ then
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi

if [[ -e $JAR_FILE ]]
then
$JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
result=$?
else
CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
export CLASSPATH

$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ActMain $*
result=$?
fi
$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE:$APPLICATION_HOME" uk.ac.sanger.artemis.components.ActMain $*
result=$?

exit $result

18 changes: 2 additions & 16 deletions art
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Expand Up @@ -143,22 +143,8 @@ then
echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi

if [[ -e $JAR_FILE ]]
then
$JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
result=$?
else
CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
export CLASSPATH

$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ArtemisMain $*
result=$?
fi
$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE:$APPLICATION_HOME" uk.ac.sanger.artemis.components.ArtemisMain $*
result=$?

exit $result

18 changes: 2 additions & 16 deletions bamview
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Expand Up @@ -81,21 +81,7 @@ then
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi

if [[ -e $JAR_FILE ]]
then
$JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
result=$?
else
CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
export CLASSPATH

$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.alignment.BamView $*
result=$?
fi
$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE:$APPLICATION_HOME" uk.ac.sanger.artemis.components.alignment.BamView $*
result=$?

exit $result
18 changes: 2 additions & 16 deletions dnaplotter
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Expand Up @@ -118,22 +118,8 @@ then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi

if [[ -e $JAR_FILE ]]
then
$JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $TEMPLATE_FILE_ARG
result=$?
else
CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar
CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
export CLASSPATH

$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?
fi
$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE:$APPLICATION_HOME" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?

exit $result

Expand Down
8 changes: 4 additions & 4 deletions etc/versions
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@@ -1,4 +1,4 @@
Artemis Release 17.0.0
ACT Release 17.0.0
DNAPlotter Release 17.0.0
BamView 17.0.0
Artemis Release 17.0.1-SNAPSHOT
ACT Release 17.0.1-SNAPSHOT
DNAPlotter Release 17.0.1-SNAPSHOT
BamView 17.0.1-SNAPSHOT
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3 changes: 0 additions & 3 deletions lib/batik/version
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3 changes: 0 additions & 3 deletions lib/picard/VERSION.txt
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