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Development setup (eclipse)

Requires Open SDK 8.

  • Type ./setup-eclipse.sh from the root of the repository
  • From eclipse:
    • Import in File menu
    • Import existing projects into workspace
    • Select the root of this repository

Development setup (CLI)

  • Type ./setup-cli.sh from the root of the repository

Running phylostream

To run PhyloModel.bl, from cli:

phylostream --engine phylostream.blang.PhyloStreamSMC --engine.nThreads Max    --engine.nParticles 100 --engine.temperatureSchedule.threshold 0.8 --model.data Synthetic --model.data.nLeaves 100 --model.data.nSites 100

From eclipse:

  • Open PhyloModel.bl
  • Right-click on the editor showing the model and select Open generated file
  • Right-click on the editor showing the generated source and select Run as Java application
  • You can now edit the command line arguments in Run > Run Configurations... > Arguments