Summary

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