Added Docker support and CI for automatic build of docker image on new

tag push. Fixed jar packaging and added resources/version.properties
file.

Author: sebeier

.github/workflows/container-release.yml

@@ -0,0 +1,52 @@
+name: Build and Publish Container Release
+
+on:
+  push:
+    tags:
+      - 'v0.*' # Triggers on tags like 0.39, 0.40 etc.
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up JDK 8
+        uses: actions/setup-java@v4
+        with:
+          java-version: '8'
+          distribution: 'temurin'
+          cache: 'maven'
+
+      - name: Build with Maven
+        run: mvn -B clean package
+
+      - name: Unzip Trimmomatic artifact
+        run: unzip target/Trimmomatic-*.zip
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract version from tag
+        id: get_version
+        # Removes 'refs/tags/' prefix to get the clean version number
+        run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ghcr.io/${{ github.repository }}:${{ steps.get_version.outputs.VERSION }}
+          build-args: |
+            TRIMMOMATIC_VERSION=${{ steps.get_version.outputs.VERSION }}

Dockerfile

@@ -0,0 +1,21 @@
+# --- Stage 1: Unpack and Prepare ---
+FROM eclipse-temurin:8-jre-focal as preparer
+# Re-declare ARG for this stage
+ARG TRIMMOMATIC_VERSION
+RUN apt-get update && apt-get install -y unzip
+WORKDIR /app
+# Copy the zip file
+COPY target/Trimmomatic-${TRIMMOMATIC_VERSION}.zip trimmomatic.zip
+RUN unzip trimmomatic.zip
+
+# --- Stage 2: Build the Final Image ---
+FROM eclipse-temurin:8-jre-focal
+# Re-declare ARG for this stage
+ARG TRIMMOMATIC_VERSION
+WORKDIR /opt/trimmomatic
+# Copy the jar file
+COPY --from=preparer /app/trimmomatic-${TRIMMOMATIC_VERSION}.jar trimmomatic.jar
+COPY --from=preparer /app/adapters ./adapters
+# MODIFIED: Specify the main class explicitly
+ENTRYPOINT ["java", "-cp", "trimmomatic.jar", "org.usadellab.trimmomatic.Trimmomatic"]
+CMD ["-version"]

pom.xml

@@ -49,6 +49,12 @@
 	</repositories>
 
     <build>
+        <resources>
+        	<resource>
+            	<directory>resources</directory>
+            	<filtering>true</filtering>
+        	</resource>
+    	</resources>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -76,6 +82,18 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+    			<groupId>org.apache.maven.plugins</groupId>
+    			<artifactId>maven-jar-plugin</artifactId>
+    			<version>3.3.0</version>
+    			<configuration>
+        			<archive>
+            			<manifest>
+                			<mainClass>org.usadellab.trimmomatic.Trimmomatic</mainClass>
+            			</manifest>
+        			</archive>
+    			</configuration>
+			</plugin>
         </plugins>
     </build>
 </project>

resources/version.properties

@@ -0,0 +1 @@
+version=${project.version}