change channel ordering to reflect current bioconda standard; pin CON…

…DA_PERL to bioconda 5.22.0

travis/deploy.sh

@@ -43,7 +43,7 @@ if [ ! -z "$ANACONDA_TOKEN" ]; then
     # Render recipe from template and dependency files, setting the tag as the current version
     conda config --set anaconda_upload yes
     python packaging/conda-recipe/render-recipe.py "$PKG_VERSION" --build-reqs requirements-conda.txt --run-reqs requirements-conda.txt --py3-run-reqs requirements-py3.txt --py2-run-reqs requirements-py2.txt --test-reqs requirements-conda-tests.txt && \
-        conda build -c broad-viral -c r -c bioconda -c conda-forge -c defaults --python "$TRAVIS_PYTHON_VERSION" --token "$ANACONDA_TOKEN" packaging/conda-recipe/viral-ngs && \
+        CONDA_PERL=5.22.0 conda build -c broad-viral -c r -c bioconda -c conda-forge -c defaults --python "$TRAVIS_PYTHON_VERSION" --token "$ANACONDA_TOKEN" packaging/conda-recipe/viral-ngs && \
         ./travis/trigger-tests-in-other-repo.sh
         # check the exit code of conda build, and if successful,
         # trigger the viral-ngs-deploy repository to test/build the docker container

travis/install-conda.sh

@@ -41,9 +41,10 @@ else # if it does not exist, we need to install miniconda
     hash -r
     conda config --set always_yes yes --set changeps1 no
     conda config --set anaconda_upload yes # for uploading packages after successful build
-    conda config --add channels bioconda
     conda config --add channels r
+    conda config --add channels defaults
     conda config --add channels conda-forge
+    conda config --add channels bioconda
     conda install --quiet -y conda #conda=4.2 # pin to 4.2.* until this is fixed: https://github.com/conda/conda-build/issues/1666
     conda config --set auto_update_conda false
     conda install --quiet -y java-jdk==8.0.112