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Quick start

After installing using one of the options mentioned in Quick Install, you're ready to run ROADIES! To get started:

Step 1: Download the test dataset (11 Drosophila genomes):**

Make sure to run this step from the main ROADIES repository directory. 

mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}'

This will save the datasets on a separate test/test_data folder within the repository

Step 2: Run the pipeline

Note

ROADIES by default runs multiple iterations for generating highly accurate trees. For quick testing, use --noconverge to run a single iteration.

Full run (multiple iterations) 

python run_roadies.py --cores 16
OR

Quick test run (one iteration) 

python run_roadies.py --cores 16 --noconverge

Step 3: Analyze Output:

  • Final UNROOTED newick tree saved as roadies.nwk in a separate output_files folder.
  • Intermediate files (if --noconverge not used) saved in a separate converge_files folder.

Note

ROADIES outputs unrooted trees by default. You can reroot trees on your own or use the provided reroot.py script in workflow/scripts/ (given a reference rooted species tree as input).