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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
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