Merge pull request #124 from urbanslug/master

Add phylogeny workflow

1 files changed, 38 insertions, 0 deletions

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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