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diff --git a/workflows/phylogeny/README.md b/workflows/phylogeny/README.md new file mode 100644 index 0000000..6ecc047 --- /dev/null +++ b/workflows/phylogeny/README.md @@ -0,0 +1,38 @@ +A workflow to generate a phylogeny that can be visualized using [auspice](https://github.com/urbanslug/auspice). +Expects a multi-fasta file path at [pggb_fasta][1] and generates a tree in `json` format. + +#### Dependencies + +Depends on: + - [pggb](https://github.com/pangenome/pggb/blob/master/pggb) + * [wfmash](https://github.com/ekg/wfmash) + * [seqwish](https://github.com/ekg/seqwish) + * [smoothxg](https://github.com/pangenome/smoothxg) + * [odgi](https://github.com/vgteam/odgi) + + - [taxophages](https://github.com/urbanslug/taxophages/) + * Clone and run with `python main.py ...` + + - [augur](https://github.com/nextstrain/augur) + + +#### Running + +Expects that taxophages is cloned in a previous dir but you can update the path [main_py_script][2] to wherever it is. + +Run the phylogeny workflow with the bleow after specifying your path to [pggb_fasta][1]. + +```bash +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 +``` + +[1]: clado-job.yml#L8 +[2]: clado-job.yml#L28 |