Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_conta…

…iner_default_channels

[18.09] Backport #7038

lib/galaxy/tools/deps/container_resolvers/__init__.py

@@ -23,15 +23,12 @@ def __init__(self, app_info=None, **kwds):
         self.app_info = app_info
         self.resolver_kwds = kwds
 
-    def _get_config_option(self, key, default=None, config_prefix=None, **kwds):
+    def _get_config_option(self, key, default=None):
         """Look in resolver-specific settings for option and then fallback to
         global settings.
         """
-        global_key = "%s_%s" % (config_prefix, key)
-        if key in kwds:
-            return kwds.get(key)
-        elif self.app_info and hasattr(self.app_info, global_key):
-            return getattr(self.app_info, global_key)
+        if self.app_info and hasattr(self.app_info, key):
+            return getattr(self.app_info, key)
         else:
             return default
 

lib/galaxy/tools/deps/container_resolvers/mulled.py

@@ -351,11 +351,11 @@ def __init__(self, app_info=None, namespace="local", hash_func="v2", **kwds):
         self.hash_func = hash_func
         self._mulled_kwds = {
             'namespace': namespace,
-            'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
             'hash_func': self.hash_func,
             'command': 'build-and-test',
         }
-        self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
+        self.auto_init = self._get_config_option("involucro_auto_init", True)
 
     def resolve(self, enabled_container_types, tool_info):
         if tool_info.requires_galaxy_python_environment:
@@ -396,13 +396,13 @@ def __init__(self, app_info=None, hash_func="v2", **kwds):
         self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
         self.hash_func = hash_func
         self._mulled_kwds = {
-            'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
             'hash_func': self.hash_func,
             'command': 'build-and-test',
             'singularity': True,
             'singularity_image_dir': self.cache_directory,
         }
-        self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
+        self.auto_init = self._get_config_option("involucro_auto_init", True)
 
     def resolve(self, enabled_container_types, tool_info):
         if tool_info.requires_galaxy_python_environment:

lib/galaxy/tools/deps/mulled/mulled_build.py

@@ -39,7 +39,7 @@
 from ..conda_compat import MetaData
 
 DIRNAME = os.path.dirname(__file__)
-DEFAULT_CHANNELS = "conda-forge,bioconda"
+DEFAULT_CHANNELS = ["conda-forge", "bioconda"]
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
 DEFAULT_WORKING_DIR = '/source/'
@@ -322,7 +322,7 @@ def add_build_arguments(parser):
                         help='quay.io namespace.')
     parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE,
                         help='Docker repository target for publication (only quay.io or compat. API is currently supported).')
-    parser.add_argument('-c', '--channels', dest='channels', default=DEFAULT_CHANNELS,
+    parser.add_argument('-c', '--channels', dest='channels', default=",".join(DEFAULT_CHANNELS),
                         help='Comma separated list of target conda channels.')
     parser.add_argument('--conda-version', dest="conda_version", default=None,
                         help="Change to specified version of Conda before installing packages.")