Merge branch 'master' of https://github.com/PoonLab/covizu

Author: ArtPoon

.gitignore

@@ -8,4 +8,5 @@ debug/*
 build/*
 dist/*
 venv/*
-
+cypress/fixtures/
+cypress/plugins/

CONTRIBUTING.md

@@ -57,4 +57,4 @@ Most web development is tested in Google Chrome.
 
 * Front-end testing is carried out using [Cypress](https://www.cypress.io/). 
 * For the purposes of this project, Cypress needs to be installed via direct download. An installation guide can be found [here](https://docs.cypress.io/guides/getting-started/installing-cypress#Direct-download). 
-* The `baseUrl` is currently set as `filogeneti.ca/covizu/`. Changes to it can be made in `Cypress.json`.
+* The `baseUrl` is currently set as `"http://127.0.0.1:8001/`. Changes to it can be made in `Cypress.json`.

batch.py

@@ -63,6 +63,9 @@ def parse_args():
     parser.add_argument('--ft2bin', default='fasttree2',
                         help='option, path to fasttree2 binary executable')
 
+    parser.add_argument('--lineages', type=str,
+                        default=os.path.join(covizu.__path__[0], "data/lineages.csv"),
+                        help="optional, path to CSV file containing Pango lineage designations.")
     parser.add_argument('--ttbin', default='treetime',
                         help='option, path to treetime binary executable')
     parser.add_argument('--clock', type=float, default=8e-4,

covizu/data/README.md

@@ -0,0 +1,5 @@
+* `problematic_sites_sarsCov2.vcf` obtained from https://github.com/W-L/ProblematicSites_SARS-CoV2 (no license)
+  - this is a listing of polymorphisms in the SARS-CoV-2 genome known to be associated with systematic experimental error (e.g., sequencing biases).
+* `lineages.csv` obtained from https://github.com/cov-lineages/pango-designation (released under Creative Commons CC-BY-NC 4.0)
+  - this is a listing of SARS-CoV-2 genome sequences associated with the designation of a new Pango lineage by Áine O'Toole, Angie Hinrichs, Rachel Colquhoun, and others.
+