Source canonical Nextstrain environment file for Travis CI

.travis.yml

@@ -10,8 +10,9 @@ before_install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - conda env create -f environment.yml
-  - source activate augur
+  - wget http://data.nextstrain.org/nextstrain.yml -O nextstrain.yml;
+  - conda env create -f nextstrain.yml
+  - source activate nextstrain
 install:
   - pip3 install -e .[dev]
 script:

README.md

@@ -50,11 +50,12 @@ Augur uses some common external bioinformatics programs which you'll need to ins
 
 Alternatively, all these dependencies (as well as augur itself) can be installed via Conda by running:
 
-    conda env create -f environment.yml
+    curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
+    conda env create -f nextstrain.yml
 
-Once installed, Conda the enviroment need to be activated whenever augur is to be used, by running:
+Once installed, the environment need to be activated whenever augur is to be used, by running:
 
-    conda activate augur
+    conda activate nextstrain
 
 ## Usage
 

docs/installation/installation.md

@@ -44,13 +44,14 @@ Other Linux distributions will likely have the same packages available, although
 
 Alternatively, augur itself and all of its dependencies can be installed into a [Conda](https://conda.io/miniconda.html) environment:
 
-    conda env create -f environment.yml
+    curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
+    conda env create -f nextstrain.yml
 
-> _By default this environment is named "augur" but you can change that by providing a name to the above command with `-n <your-env-name>`_
+> _By default this environment is named "nextstrain" but you can change that by providing a name to the above command with `-n <your-env-name>`_
 
-When that finishes, the enviroment needs to be activated whenever you want to use augur:
+When that finishes, the environment needs to be activated whenever you want to use augur:
 
-    conda activate augur
+    conda activate nextstrain
 
 ## Install from source