A workflow to generate a phylogeny that can be visualized using auspice.
Expects a multi-fasta file path at pggb_fasta and generates a tree in json format.
Dependencies
Depends on: - pggb * wfmash * seqwish * smoothxg * odgi
- taxophages
-
Clone and run with
python main.py ...
Running
Expects that taxophages is cloned in a previous dir but you can update the path main_py_script to wherever it is.
Run the phylogeny workflow with the bleow after specifying your path to pggb_fasta.
R_PACKAGES="${HOME}/RLibraries" \ # a directory holding R packages. Needed if R packages installed using install.packages on server e.g https://github.com/urbanslug/taxophages/blob/master/scripts/deps.R
TAXOPHAGES_ENV=server \ # helps taxophages figure out where it is being ran
AUGUR_RECURSION_LIMIT=30000 \ # augur isn't used to working with so many nested values
cwltool --preserve-entire-environment --no-container phylogeny.cwl clado-job.yml
Alternatively run any workflow with
cwltool --no-container <workflow>.cwl clado-job.yml