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Migrate Docker builds to custom Dockerfiles and update exomiser script #628

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0e972ff
feat: Migrate Docker image builds from Jib to custom Dockerfiles usin…
matthdsm Mar 6, 2026
940c2ea
fix enable_exomiser script causing bash to exit
matthdsm Mar 7, 2026
77fe888
feat: Replace `enable_exomiser.sh` alias with a `exomiser` launcher …
matthdsm Mar 7, 2026
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71 changes: 71 additions & 0 deletions exomiser-cli/exomiser
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@@ -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[@]}"
33 changes: 33 additions & 0 deletions exomiser-cli/exomiser-bash.dockerfile
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# 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
32 changes: 32 additions & 0 deletions exomiser-cli/exomiser-distroless.dockerfile
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# 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"]
119 changes: 34 additions & 85 deletions exomiser-cli/pom.xml
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Expand Up @@ -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>
Expand All @@ -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>
Expand Down
4 changes: 0 additions & 4 deletions exomiser-cli/src/main/jib/enable_exomiser.sh
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Empty file modified mvnw
100644 → 100755
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