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BEAST 2 Docker and Apptainer\n\nDocker and Apptainer setup for the BEAST 2 software \n\n# Table of contents\n\n- [BEAST 2 Docker and Apptainer](#beast-2-docker-and-apptainer)\n- [Table of contents](#table-of-contents)\n- [Docker](#docker)\n- [Apptainer](#apptainer)\n\n# Docker\n\nPull the Docker image:\n\n```\n./workspace/scripts/pull.sh \n```\n\nRun BEAST2:\n\n```\ncd workspace\n./scripts/run.sh examples/testRNA.xml\n```\n\nRun BEAST2 with BEAGLE:\n\n```\ncd workspace\n./scripts/run.sh -beagle -beagle_SSE -beagle_CPU -threads 4 examples/testRNA.xml\n```\n\n# Apptainer\n\nBuild the Apptainer image:\n\n```\n./workspace/scripts/apptainer_build.sh \n```\n\nRun BEAST2:\n\n```\n./beast2.sif workspace/examples/testRNA.xml\n```\n\nRun BEAST2 with BEAGLE:\n\n```\n./beast2.sif -beagle -beagle_SSE -beagle_CPU -threads 4 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