update channel order, see bioconda#2675

.travis.yml

@@ -11,7 +11,7 @@ env:
   global:
   - secure: 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
   - SUBDAGS=2
-  - BIOCONDA_UTILS_TAG=4f15d98fcc3e7834ee7efbac9bd0b6fa4d5f4569
+  - BIOCONDA_UTILS_TAG=01d72be386da6ff5e596c8f31b36db49a9f5ba4c
   - BIOCONDA_UTILS_ARGS="--loglevel=info --mulled-test"
   matrix:
   - SUBDAG=0

README.md

@@ -64,14 +64,20 @@ When the recipe is ready, first test it with your local conda installation via
 Bioconda uses the `bioconda`, `r`, and `conda-forge` channels. You can either
 set them globally with:
 ```
-conda config --add channels bioconda
-conda config --add channels r
 conda config --add channels conda-forge
+conda config --add channels defaults
+conda config --add channels r
+conda config --add channels bioconda
+
 ```
 
 or by adding the channels to the build command:
 
-    conda build recipes/your_package --channel bioconda --channel r --channel conda-forge
+    conda build recipes/your_package \
+        --channel conda-forge \
+        --channel defaults \
+        --channel r \
+        --channel bioconda
 
 Then, you can test the build in a docker container. The authoritative source
 for how packages are built can be found in the `scripts/travis-run.sh` script,

config.yml

@@ -5,8 +5,8 @@ blacklists:
 
 docker_image: "condaforge/linux-anvil"
 channels:
-    - anaconda
-    - r
+    - defaults
     - conda-forge
+    - r
     - bioconda
 docker_client_version: '1.20'

scripts/travis-setup.sh

@@ -17,16 +17,18 @@ sudo chown -R $USER /anaconda
 export PATH=/anaconda/bin:$PATH
 conda update -y conda
 
-# setup bioconda channel
-conda config --add channels anaconda
-conda config --add channels r
+# channels are added from lowest to highest priority
 conda config --add channels conda-forge
+conda config --add channels defaults
+conda config --add channels r
 conda config --add channels bioconda
 
+
 conda install -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/conda-requirements.txt
 
 conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
 conda config --add channels file://anaconda/conda-bld
+conda config --get
 
 # setup bioconda-utils
 pip install git+https://github.com/bioconda/bioconda-utils.git@$BIOCONDA_UTILS_TAG