Default shed tool installation to database/shed_tools instead of

../shed_tools

config/migrated_tools_conf.xml.sample

@@ -1,3 +1,3 @@
 <?xml version="1.0"?>
-<toolbox tool_path="../shed_tools">
-</toolbox>
+<toolbox tool_path="database/shed_tools">
+</toolbox>

config/shed_tool_conf.xml.sample

@@ -1,3 +1,3 @@
 <?xml version="1.0"?>
-<toolbox tool_path="../shed_tools">
+<toolbox tool_path="database/shed_tools">
 </toolbox>

doc/source/admin/tool_panel.rst

@@ -37,7 +37,7 @@ Sections & Labels
 .. code-block:: xml
 
     <?xml version="1.0"?>
-    <toolbox tool_path="../shed_tools">
+    <toolbox tool_path="database/shed_tools">
         <section id="mts" name="MTS" version="">
           <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fastqc/rgFastQC.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67" labels="new">
               <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
@@ -48,4 +48,4 @@ Sections & Labels
                 <version>0.67</version>
             </tool>
         </section>
-    </toolbox>
+    </toolbox>

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -38,8 +38,8 @@ def get_message_for_no_shed_tool_config():
     message = 'The tool_config_file setting in galaxy.ini must include at least one shed tool configuration file name with a <toolbox> '
     message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
     message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
-    message += '<toolbox tool_path="../shed_tools">).  For details, see the "Installation of Galaxy tool shed repository tools into a local '
-    message += 'Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
+    message += '<toolbox tool_path="database/shed_tools">).  For details, see the "Installation of Galaxy tool shed repository tools into a '
+    message += 'local Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
     return message
 
 
@@ -517,8 +517,8 @@ def install_repository_revision(self, trans, payload, **kwd):
                                           (e.g., galaxy.ini).  At least one shed-related tool panel config file is required to be configured. Setting
                                           this parameter to a specific file enables you to choose where the specified repository will be installed because
                                           the tool_path attribute of the <toolbox> from the specified file is used as the installation location
-                                          (e.g., <toolbox tool_path="../shed_tools">).  If this parameter is not set, a shed-related tool panel configuration
-                                          file will be selected automatically.
+                                          (e.g., <toolbox tool_path="database/shed_tools">).  If this parameter is not set, a shed-related tool panel
+                                          configuration file will be selected automatically.
         """
         # Get the information about the repository to be installed from the payload.
         tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(payload, include_changeset=True)
@@ -573,8 +573,8 @@ def install_repository_revisions(self, trans, payload, **kwd):
                                           (e.g., galaxy.ini).  At least one shed-related tool panel config file is required to be configured. Setting
                                           this parameter to a specific file enables you to choose where the specified repository will be installed because
                                           the tool_path attribute of the <toolbox> from the specified file is used as the installation location
-                                          (e.g., <toolbox tool_path="../shed_tools">).  If this parameter is not set, a shed-related tool panel configuration
-                                          file will be selected automatically.
+                                          (e.g., <toolbox tool_path="database/shed_tools">).  If this parameter is not set, a shed-related tool panel
+                                          configuration file will be selected automatically.
         """
         self.__ensure_can_install_repos(trans)
         # Get the information about all of the repositories to be installed.

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -815,7 +815,7 @@ def prepare_for_install(self, trans, **kwd):
             message += 'shed tool configuration file name with a <b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> '
             message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
             message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
-            message += 'whose <b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
+            message += 'whose <b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="database/shed_tools"&gt;</b>).<p/>See the '
             message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
             message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
             message += 'Shed wiki for all of the details.'

lib/tool_shed/galaxy_install/migrate/check.py

@@ -79,8 +79,8 @@ def verify_tools(app, url, galaxy_config_file=None, engine_options={}):
                     msg += "be removed from your file%s named %s.\n\n" % (plural, tool_panel_config_file_names)
                     msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n"
                     msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n"
-                    msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">).  The default location\n'
-                    msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n"
+                    msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="database/shed_tools">).  The default location\n'
+                    msg += "setting is 'database/shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n"
                     msg += "you execute the installation process if appropriate.  The configured location must be outside of the Galaxy installation\n"
                     msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n"
                     msg += "the Galaxy installation directory hierarchy.  This is because tool shed repositories will be installed using mercurial's\n"

lib/tool_shed/util/common_util.py

@@ -140,7 +140,7 @@ def get_non_shed_tool_panel_configs(app):
     config_filenames = []
     for config_filename in app.config.tool_configs:
         # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related.
-        # <toolbox tool_path="../shed_tools">
+        # <toolbox tool_path="database/shed_tools">
         tree, error_message = xml_util.parse_xml(config_filename)
         if tree is None:
             continue