geneious-plugin-preprocessing/build.xml at main · dhoconno/geneious-plugin-preprocessing · GitHub

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<?xml version="1.0" ?>

<project name="FastpPlugin" default="distribute" basedir=".">

    <property file="plugin.properties"/>
    <property name="build" location="build"/>
    <property name="classes" location="classes"/>
    <property name="src" location="src"/>
    <property name="java-src" location="src/com"/>
    <property name="resources" location="src/main/resources"/>
    <property name="devkit" location="/Users/dho/Downloads/geneious-2025.2.2-devkit"/>

    <!-- Define classpath to include all required Geneious API JARs -->
    <path id="classpath">
        <fileset dir="${devkit}/examples/GeneiousFiles/lib">
            <include name="GeneiousPublicAPI.jar"/>
            <include name="jdom.jar"/>
            <include name="jebl.jar"/>
            <include name="commons-io-*.jar"/>
            <include name="commons-lang3-*.jar"/>
        </fileset>
    </path>

    <!-- Main distribution target - creates the .gplugin file with all binaries -->
    <target name="distribute" depends="build">
        <copy file="${build}/${short-plugin-name}.jar" tofile="${build}/${short-plugin-name}.gplugin"/>
        <echo message="Created ${build}/${short-plugin-name}.gplugin"/>
        <echo message="Install this plugin in Geneious by copying it to the Geneious plugins directory"/>
    </target>

    <!-- Build skinny version - JAR without bundled binaries (for users who install tools separately) -->
    <target name="build-skinny" depends="compile">
        <jar jarfile="${build}/${short-plugin-name}-skinny.jar">
            <!-- Compiled Java classes -->
            <fileset dir="${classes}"/>

            <!-- Resources WITHOUT binaries - excludes fastp, fastplong, BBTools, seqkit -->
            <fileset dir="${resources}">
                <include name="**/*"/>
                <exclude name="binaries/**"/>
            </fileset>

            <!-- Plugin configuration -->
            <fileset dir="">
                <include name="plugin.properties"/>
            </fileset>
        </jar>
    </target>

    <!-- Skinny distribution target - creates .gplugin without binaries -->
    <target name="distribute-skinny" depends="build-skinny">
        <copy file="${build}/${short-plugin-name}-skinny.jar" tofile="${build}/${short-plugin-name}-skinny.gplugin"/>
        <echo message=""/>
        <echo message="========================================"/>
        <echo message="Created SKINNY plugin: ${build}/${short-plugin-name}-skinny.gplugin"/>
        <echo message="========================================"/>
        <echo message=""/>
        <echo message="IMPORTANT: This skinny version does NOT include bundled binaries."/>
        <echo message="Users must install the following tools separately:"/>
        <echo message="  - fastp/fastplong"/>
        <echo message="  - BBTools suite"/>
        <echo message="  - seqkit"/>
        <echo message=""/>
        <echo message="See README.md for installation instructions."/>
        <echo message="========================================"/>
        <echo message=""/>
    </target>

    <!-- Build target - creates the JAR file with compiled classes, resources, and plugin.properties -->
    <target name="build" depends="compile">
        <jar jarfile="${build}/${short-plugin-name}.jar">
            <!-- Compiled Java classes -->
            <fileset dir="${classes}"/>

            <!-- All resources including binaries for:
                 - fastp and fastplong (macos)
                 - BBTools suite (macos): shell scripts, compiled .class files in current/ directory
                 - seqkit (macos)
            -->
            <fileset dir="${resources}">
                <include name="**/*"/>
            </fileset>

            <!-- Plugin configuration -->
            <fileset dir="">
                <include name="plugin.properties"/>
            </fileset>
        </jar>
    </target>

    <!-- Compile Java sources targeting Java 11 (Geneious requirement) -->
    <target name="compile" depends="prepare">
        <javac target="11" source="11" destdir="${classes}" debug="true" includeantruntime="false">
            <classpath refid="classpath"/>
            <!-- Only compile Java sources from src/com, excluding resources -->
            <src path="${java-src}"/>
        </javac>
    </target>

    <!-- Prepare build directories -->
    <target name="prepare">
        <mkdir dir="${build}"/>
        <mkdir dir="${classes}"/>
    </target>

    <!-- Clean build artifacts -->
    <target name="clean">
        <delete dir="${build}"/>
        <delete dir="${classes}"/>
    </target>

    <!-- Test target - useful for running quick checks -->
    <target name="test" depends="compile">
        <echo message="Compilation successful. Plugin classes are ready."/>
    </target>

</project>