Change conda channel priority: conda-forge > bioconda

xref. bioconda/bioconda-utils#330

doc/source/admin/conda_faq.rst

@@ -227,9 +227,9 @@ Admin panel (under Tool Management → Manage dependencies).
 The simple answer is: you don't need to do much to make Conda work for a tool.
 
 The ``<requirement>`` tag in the tool XML file is enough. The name and the
-version should correspond to a Conda package in the ``default``, ``r``,
-``bioconda`` or ``iuc`` Conda channel (you can extend this list if you
-like in your ``galaxy.yml`` ). If this is the case you are ready to go. Read
+version should correspond to a Conda package in one of the enabled channels
+(which are specified by the ``conda_ensure_channels`` directive in
+``galaxy.yml`` ). If this is the case you are ready to go. Read
 more about `Conda channels`_  and browse their packages on https://anaconda.org/ url followed by the channel name (e.g.
 `https://anaconda.org/bioconda <https://anaconda.org/bioconda>`__
 ).
@@ -258,7 +258,7 @@ With Conda package manager installed on your system, run:
 
 .. code-block:: bash
 
-   $ conda search <package_name> -c bioconda -c iuc
+   $ conda search <package_name> -c iuc -c conda-forge -c bioconda
 
 This will search in all channels that are activated by default in
 Galaxy. If you find your package, you are ready to go. If not please

doc/source/admin/dependency_resolvers.rst

@@ -218,7 +218,7 @@ debug
 ensure_channels
     conda channels to enable by default. See
     https://conda.io/docs/user-guide/tasks/manage-channels.html for more
-    information about channels. This defaults to ``iuc,bioconda,conda-forge,defaults``.
+    information about channels. This defaults to ``iuc,conda-forge,bioconda,defaults``.
     This order should be consistent with the `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__
     if it includes ``bioconda``.
 

doc/source/admin/framework_dependencies.rst

@@ -204,8 +204,8 @@ not run the script, the dependencies will simply be installed via pip.
 
 .. code-block:: console
 
-    $ conda config --add channels conda-forge
     $ conda config --add channels bioconda
+    $ conda config --add channels conda-forge
     $ conda create --name galaxy --file <(lib/galaxy/dependencies/conda-file.sh)
     Filtering out requirements not available in conda... done
     Solving environment: done

lib/galaxy/dependencies/conda-file.sh

@@ -6,7 +6,7 @@
 #
 # You should use this script like so:
 #
-# conda create --override-channels -c bioconda -c conda-forge -c defaults \
+# conda create --override-channels -c conda-forge -c bioconda -c defaults \
 #     -n <env> --file <(lib/galaxy/dependencies/conda-file.sh) python=2.7
 
 here=$(dirname $0)
@@ -19,7 +19,7 @@ fi
 
 printf "Filtering out Galaxy requirements not available from Conda:" >&2
 egrep -iv $( \
-    conda create --override-channels -c bioconda -c conda-forge -c defaults \
+    conda create --override-channels -c conda-forge -c bioconda -c defaults \
         -n _gx_test_env --dry-run --file <(sed 's/;.*//' $here/pinned-requirements.txt) python=2.7 2>&1 \
         | grep '^\s*-' | grep -v https: | awk '{print $NF}' | paste -s -d'|' \
 ) $here/pinned-requirements.txt | sed 's/;.*//'

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -271,7 +271,7 @@ mapping:
 
       conda_ensure_channels:
         type: str
-        default: iuc,bioconda,conda-forge,defaults
+        default: iuc,conda-forge,bioconda,defaults
         required: false
         desc: |
           conda channels to enable by default