Update conda channel order to sync with Bioconda

config/galaxy.ini.sample

@@ -209,8 +209,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Pass debug flag to conda commands.
 #conda_debug = False
 # conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html)
-# the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8)
-#conda_ensure_channels = iuc,bioconda,r,defaults,conda-forge
+#conda_ensure_channels = iuc,bioconda,conda-forge,defaults,r
 # Set to True to instruct Galaxy to look for and install missing tool
 # dependencies before each job runs.
 #conda_auto_install = False

doc/source/admin/dependency_resolvers.rst

@@ -220,8 +220,8 @@ debug
 ensure_channels
     conda channels to enable by default. See
     http://conda.pydata.org/docs/custom-channels.html for more
-    information about channels. This defaults to ``iuc,bioconda,r,defaults,conda-forge``.
-    This order should be consistent with `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8>`__
+    information about channels. This defaults to ``iuc,bioconda,conda-forge,defaults,r``.
+    This order should be consistent with the `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__
     if it includes ``bioconda``.
 
 auto_install

lib/galaxy/tools/deps/resolvers/conda.py

@@ -39,7 +39,11 @@
 
 DEFAULT_BASE_PATH_DIRECTORY = "_conda"
 DEFAULT_CONDARC_OVERRIDE = "_condarc"
-DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,r,defaults,conda-forge"
+# Conda channel order from highest to lowest, following the one used in
+# https://github.com/bioconda/bioconda-recipes/blob/master/config.yml , but
+# adding `iuc` as first channel (for Galaxy-specific packages) and `r` as last
+# (for old R packages)
+DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,conda-forge,defaults,r"
 CONDA_SOURCE_CMD = """[ "$CONDA_DEFAULT_ENV" = "%s" ] ||
 MAX_TRIES=3
 COUNT=0