Merge branch 'release_19.09' into release_20.01

doc/source/admin/galaxy_options.rst

@@ -780,6 +780,17 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``build_sites_config_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    File that defines the builds (dbkeys) available at sites used by
+    display applications and the URL to those sites.
+:Default: ``config/build_sites.yml.sample``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~
 ``builds_file_path``
 ~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config/sample/galaxy.yml.sample

@@ -488,6 +488,10 @@ galaxy:
   # scenarios than the watchdog default.
   #watch_tool_data_dir: 'false'
 
+  # File that defines the builds (dbkeys) available at sites used by
+  # display applications and the URL to those sites.
+  #build_sites_config_file: config/build_sites.yml.sample
+
   # File containing old-style genome builds.
   # The value of this option will be resolved with respect to
   # <tool_data_path>.

lib/galaxy/model/tool_shed_install/__init__.py

@@ -137,7 +137,7 @@ class ToolShedRepository(object):
                 self.shed_config_filename = shed_tool_conf_dict['config_filename']
                 return shed_tool_conf_dict
         # Very last resort, get default shed_tool_config file for this instance
-        shed_tool_conf_dict = self.app.toolbox.default_shed_tool_conf_dict()
+        shed_tool_conf_dict = app.toolbox.default_shed_tool_conf_dict()
         self.shed_config_filename = shed_tool_conf_dict['config_filename']
         return shed_tool_conf_dict
 

lib/galaxy/tools/__init__.py

@@ -165,7 +165,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "lastz_paired_reads_wrapper",
     "subRate1",
     "substitutions1",
-    "sam_pileup",
     "find_diag_hits",
     "cufflinks",
     # Tools improperly migrated to the tool shed (iuc)
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "lastz_wrapper_2": packaging.version.parse("1.3"),
     "PEsortedSAM2readprofile": packaging.version.parse("1.1.1"),
     "sam_to_bam": packaging.version.parse("1.1.3"),
+    "sam_pileup": packaging.version.parse("1.1.3"),
 }
 
 

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -587,6 +587,14 @@ mapping:
           will use a less efficient monitoring scheme that may work in wider range of scenarios than
           the watchdog default.
 
+      build_sites_config_file:
+        type: str
+        default: config/build_sites.yml.sample
+        required: false
+        desc: |
+          File that defines the builds (dbkeys) available at sites used by display applications
+          and the URL to those sites.
+
       builds_file_path:
         type: str
         default: shared/ucsc/builds.txt