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

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matthdsm wants to merge 3 commits intoexomiser:masterfrom
matthdsm:fix/docker
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Migrate Docker builds to custom Dockerfiles and update exomiser script#628
matthdsm wants to merge 3 commits intoexomiser:masterfrom
matthdsm:fix/docker

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@matthdsm matthdsm commented Mar 7, 2026

This pull request introduces a new approach for building and running Docker images for the exomiser-cli application, replacing the previous Jib-based method with custom Dockerfiles and Maven plugin configuration. The changes streamline the build process, provide more flexibility for runtime environments, and add a robust executable launch script for the CLI.

Docker build and runtime improvements:

  • Added two custom Dockerfiles: exomiser-bash.dockerfile for a Bash-based runtime and exomiser-distroless.dockerfile for a minimal distroless runtime, both including explicit build and copy steps for the CLI jar and dependencies. [1] [2]
  • Replaced the Jib Maven plugin with the exec-maven-plugin in pom.xml to build Docker images using the custom Dockerfiles, supporting multiple tags and image variants. [1] [2]

Executable script enhancements:

  • Introduced a new exomiser Bash script for launching the CLI, which intelligently determines the Java executable, parses JVM and application arguments, and locates the jar file, improving usability and portability.

Cleanup and deprecation:

  • Removed the old enable_exomiser.sh script, which relied on Bash aliasing and Jib-generated files, as it is superseded by the new launch script and Docker setup.

@matthdsm matthdsm mentioned this pull request Mar 7, 2026
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