diff --git a/exomiser-cli/exomiser b/exomiser-cli/exomiser
new file mode 100644
index 000000000..55212607d
--- /dev/null
+++ b/exomiser-cli/exomiser
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+# ==========================================
+# Exomiser executable launch script
+# ==========================================
+
+# Determine the Java command to use to start the JVM.
+if [[ -n "$EXOMISER_JAVA_HOME" ]]; then
+  JAVA_CMD="$EXOMISER_JAVA_HOME/bin/java"
+elif [[ -n "$JAVA_HOME" ]]; then
+  JAVA_CMD="$JAVA_HOME/bin/java"
+elif [ -x /usr/libexec/java_home ]; then
+  JAVA_CMD="$(/usr/libexec/java_home -v 17+ 2>/dev/null)/bin/java" || JAVA_CMD=java
+else
+  JAVA_CMD="$(which java)" || JAVA_CMD=java
+fi
+
+if [ ! -x "$JAVA_CMD" ] && ! command -v "$JAVA_CMD" &> /dev/null; then
+    echo "ERROR: Cannot find 'java'. Please make sure Java 17+ is installed." >&2
+    exit 1
+fi
+
+declare -a JVM_OPTS=()
+declare -a ARGS=()
+
+# Parse command line arguments to split JVM options from Exomiser arguments
+while [[ $# -gt 0 ]]; do
+    case $1 in
+    -D*|-X*)
+      JVM_OPTS+=("$1")
+      ;;
+    *)
+      ARGS+=("$1")
+      ;;
+    esac
+    shift
+done
+
+# Mix in global JAVA_OPTS and EXOMISER_OPTS if they are set
+if [[ -n "$JAVA_OPTS" ]]; then
+    read -a GLOBAL_JAVA_OPTS <<< "$JAVA_OPTS"
+    JVM_OPTS+=("${GLOBAL_JAVA_OPTS[@]}")
+fi
+if [[ -n "$EXOMISER_OPTS" ]]; then
+    read -a GLOBAL_EXO_OPTS <<< "$EXOMISER_OPTS"
+    JVM_OPTS+=("${GLOBAL_EXO_OPTS[@]}")
+fi
+
+# Determine the path to the jar
+# It could be explicitly defined by EXOMISER_JAR
+if [ -z "$EXOMISER_JAR" ]; then
+    # Default location inside the Docker container
+    if [ -f "/app/exomiser-cli.jar" ]; then
+        EXOMISER_JAR="/app/exomiser-cli.jar"
+    else
+        # Fallback: resolve relative to this script
+        SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+        if [ -f "$SCRIPT_DIR/../exomiser-cli.jar" ]; then
+            EXOMISER_JAR="$SCRIPT_DIR/../exomiser-cli.jar"
+        elif [ -f "$SCRIPT_DIR/exomiser-cli.jar" ]; then
+            EXOMISER_JAR="$SCRIPT_DIR/exomiser-cli.jar"
+        else
+            echo "ERROR: Cannot find exomiser-cli.jar." >&2
+            echo "Please set EXOMISER_JAR to the location of the jar file." >&2
+            exit 1
+        fi
+    fi
+fi
+
+# Execute the application
+exec "$JAVA_CMD" "${JVM_OPTS[@]}" -jar "$EXOMISER_JAR" "${ARGS[@]}"
diff --git a/exomiser-cli/exomiser-bash.dockerfile b/exomiser-cli/exomiser-bash.dockerfile
new file mode 100644
index 000000000..bb2b083f1
--- /dev/null
+++ b/exomiser-cli/exomiser-bash.dockerfile
@@ -0,0 +1,33 @@
+# Stage 1: Build the exomiser-cli application
+FROM eclipse-temurin:21-jdk AS builder
+
+# Set the working directory
+WORKDIR /build
+
+# Copy the maven wrapper and pom files
+COPY mvnw .
+COPY . .
+
+# Build and install phenix-repository to local maven repo first
+RUN ./mvnw install -DskipTests -pl phenix-repository -am
+
+# Build only the CLI and its dependencies
+RUN ./mvnw clean package -DskipTests -pl exomiser-cli -am
+
+# Stage 2: Create the runtime bash image
+# Use eclipse-temurin:25.0.2_10-jre as requested
+FROM eclipse-temurin:25.0.2_10-jre
+
+# Define volumes
+VOLUME ["/exomiser-data", "/exomiser", "/results"]
+
+# Set the working directory
+WORKDIR /app
+
+# Copy the built jar and its dependencies
+COPY --from=builder /build/exomiser-cli/target/exomiser-cli-*.jar /app/exomiser-cli.jar
+COPY --from=builder /build/exomiser-cli/target/lib /app/lib
+
+# Copy executable exomiser script and make it available on the PATH
+COPY exomiser-cli/exomiser /usr/local/bin/exomiser
+RUN chmod +x /usr/local/bin/exomiser
diff --git a/exomiser-cli/exomiser-distroless.dockerfile b/exomiser-cli/exomiser-distroless.dockerfile
new file mode 100644
index 000000000..d932fb80b
--- /dev/null
+++ b/exomiser-cli/exomiser-distroless.dockerfile
@@ -0,0 +1,32 @@
+# Stage 1: Build the exomiser-cli application
+FROM eclipse-temurin:21-jdk AS builder
+
+# Set the working directory
+WORKDIR /build
+
+# Copy the maven wrapper and pom files
+COPY mvnw .
+COPY . .
+
+# Build and install phenix-repository to local maven repo first
+RUN ./mvnw install -DskipTests -pl phenix-repository -am
+
+# Build only the CLI and its dependencies
+RUN ./mvnw clean package -DskipTests -pl exomiser-cli -am
+
+# Stage 2: Create the runtime distroless image
+# Use the base image defined in pom.xml docker.base.image
+FROM gcr.io/distroless/java25-debian13@sha256:4eadd00d3bff73e6a7491dd36653c1d318ac93fb1fb2cd5eef768fd2b4238408
+
+# Define volumes
+VOLUME ["/exomiser-data", "/exomiser", "/results"]
+
+# Set the working directory
+WORKDIR /app
+
+# Copy the built jar and its dependencies
+COPY --from=builder /build/exomiser-cli/target/exomiser-cli-*.jar /app/exomiser-cli.jar
+COPY --from=builder /build/exomiser-cli/target/lib /app/lib
+
+# Run the jar
+ENTRYPOINT ["java", "-jar", "/app/exomiser-cli.jar"]
diff --git a/exomiser-cli/pom.xml b/exomiser-cli/pom.xml
index 2782cea93..8566b0e00 100644
--- a/exomiser-cli/pom.xml
+++ b/exomiser-cli/pom.xml
@@ -215,63 +215,28 @@
             <build>
                 <plugins>
                     <plugin>
-                        <groupId>com.google.cloud.tools</groupId>
-                        <artifactId>jib-maven-plugin</artifactId>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>exec-maven-plugin</artifactId>
+                        <version>3.5.0</version>
                         <executions>
                             <execution>
                                 <id>build-docker-image</id>
                                 <phase>package</phase>
                                 <goals>
-                                    <goal>build</goal>
+                                    <goal>exec</goal>
                                 </goals>
                                 <configuration>
-                                    <from>
-                                        <image>
-                                            ${docker.base.image}
-                                        </image>
-                                        <platforms>
-                                            <platform>
-                                                <os>linux</os>
-                                                <architecture>arm64</architecture>
-                                            </platform>
-                                            <!-- No longer provided was this for MacOS? -->
-<!--                                            <platform>-->
-<!--                                                <os>linux</os>-->
-<!--                                                <architecture>arm</architecture>-->
-<!--                                            </platform>-->
-                                            <platform>
-                                                <os>linux</os>
-                                                <architecture>amd64</architecture>
-                                            </platform>
-                                        </platforms>
-                                    </from>
-                                    <to>
-                                        <image>
-                                            ${docker.registry}/${docker.repository}/${project.artifactId}:${project.parent.version}-bash
-                                        </image>
-                                        <tags>
-                                            <tag>latest-bash</tag>
-                                            <tag>${project.parent.version}-bash</tag>
-                                        </tags>
-                                    </to>
-                                    <container>
-                                        <entrypoint>
-                                            <arg>/bin/bash</arg>
-                                        </entrypoint>
-                                        <volumes>
-                                            <volume>/exomiser-data</volume>
-                                            <volume>/exomiser</volume>
-                                            <volume>/results</volume>
-                                        </volumes>
-                                    </container>
-                                    <extraDirectories>
-                                        <permissions>
-                                            <permission>
-                                                <file>/entrypoint.sh</file>
-                                                <mode>755</mode>
-                                            </permission>
-                                        </permissions>
-                                    </extraDirectories>
+                                    <executable>docker</executable>
+                                    <arguments>
+                                        <argument>build</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:${project.parent.version}-bash</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:latest-bash</argument>
+                                        <argument>-f</argument>
+                                        <argument>exomiser-bash.dockerfile</argument>
+                                        <argument>..</argument>
+                                    </arguments>
                                 </configuration>
                             </execution>
                         </executions>
@@ -284,48 +249,32 @@
             <build>
                 <plugins>
                     <plugin>
-                        <groupId>com.google.cloud.tools</groupId>
-                        <artifactId>jib-maven-plugin</artifactId>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>exec-maven-plugin</artifactId>
+                        <version>3.5.0</version>
                         <executions>
                             <execution>
                                 <id>build-docker-image</id>
                                 <phase>package</phase>
                                 <goals>
-                                    <goal>build</goal>
+                                    <goal>exec</goal>
                                 </goals>
                                 <configuration>
-                                    <from>
-                                        <image>
-                                            ${docker.base.image}
-                                        </image>
-                                        <platforms>
-                                            <platform>
-                                                <os>linux</os>
-                                                <architecture>arm64</architecture>
-                                            </platform>
-                                            <platform>
-                                                <os>linux</os>
-                                                <architecture>amd64</architecture>
-                                            </platform>
-                                        </platforms>
-                                    </from>
-                                    <to>
-                                        <image>
-                                            ${docker.registry}/${docker.repository}/${project.artifactId}:${project.parent.version}
-                                        </image>
-                                        <tags>
-                                            <tag>latest</tag>
-                                            <tag>latest-distroless</tag>
-                                            <tag>${project.parent.version}-distroless</tag>
-                                        </tags>
-                                    </to>
-                                    <container>
-                                        <volumes>
-                                            <volume>/exomiser-data</volume>
-                                            <volume>/exomiser</volume>
-                                            <volume>/results</volume>
-                                        </volumes>
-                                    </container>
+                                    <executable>docker</executable>
+                                    <arguments>
+                                        <argument>build</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:${project.parent.version}</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:latest</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:latest-distroless</argument>
+                                        <argument>-t</argument>
+                                        <argument>${docker.registry}/${docker.repository}/${project.artifactId}:${project.parent.version}-distroless</argument>
+                                        <argument>-f</argument>
+                                        <argument>exomiser-distroless.dockerfile</argument>
+                                        <argument>..</argument>
+                                    </arguments>
                                 </configuration>
                             </execution>
                         </executions>
diff --git a/exomiser-cli/src/main/jib/enable_exomiser.sh b/exomiser-cli/src/main/jib/enable_exomiser.sh
deleted file mode 100755
index 8027a37bb..000000000
--- a/exomiser-cli/src/main/jib/enable_exomiser.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-
-# Assumes `java` is on PATH in the base image.
-alias exomiser="exec java $JAVA_OPTS -cp $( cat /app/jib-classpath-file ) $( cat /app/jib-main-class-file )"
diff --git a/mvnw b/mvnw
old mode 100644
new mode 100755