commit/galaxy-central: greg: Enhancements related to displaying tool shed repository contents and dependencies in both Galaxy and the tool shed

30 Nov 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/14589278b02d/
changeset:   14589278b02d
user:        greg
date:        2012-11-30 21:14:26
summary:     Enhancements related to displaying tool shed repository contents and dependencies in both Galaxy and the tool shed
affected #:  35 files

diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3111,8 +3111,6 @@
                 if os.path.exists( relative_path ):
                     self.shed_config_filename = shed_tool_conf_dict[ 'config_filename' ]
                     return shed_tool_conf_dict
-        #if self.dist_to_shed:
-        #    #return ./migrated_tools.xml
         return default
     def get_shed_config_dict( self, app, default=None ):
         """
@@ -3154,8 +3152,8 @@
     def in_error_state( self ):
         return self.status == self.installation_status.ERROR
     @property
-    def has_readme( self ):
-        return self.metadata and 'readme' in self.metadata
+    def has_readme_files( self ):
+        return self.metadata and 'readme_files' in self.metadata
     @property
     def installed_tool_dependencies( self ):
         """Return the repository's tool dependencies that are currently installed."""


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/tool_shed/install_manager.py
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -6,7 +6,6 @@
 from galaxy.tools import ToolSection
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
-from galaxy.util.shed_util_common import *
 from galaxy.util.odict import odict
 from galaxy.tool_shed.common_util import *
 


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/tool_shed/update_manager.py
--- a/lib/galaxy/tool_shed/update_manager.py
+++ b/lib/galaxy/tool_shed/update_manager.py
@@ -4,7 +4,6 @@
 import threading, urllib2, logging
 from galaxy.util import string_as_bool
 from galaxy.util.shed_util import *
-from galaxy.util.shed_util_common import *
 
 log = logging.getLogger( __name__ )
 


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -33,7 +33,6 @@
 from galaxy.util.hash_util import *
 from galaxy.util import listify
 from galaxy.util.shed_util import *
-from galaxy.util.shed_util_common import *
 from galaxy.web import url_for
 
 from galaxy.visualization.genome.visual_analytics import TracksterConfig


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1,10 +1,11 @@
-import os, shutil, tempfile, logging, string
+import os, shutil, tempfile, logging, string, threading
 from galaxy import util
 from galaxy.tools import parameters
 from galaxy.util import inflector
 from galaxy.util.json import *
 from galaxy.web import url_for
 from galaxy.web.form_builder import SelectField
+from galaxy.webapps.community.util.container_util import *
 from galaxy.datatypes.checkers import *
 from galaxy.model.orm import *
 
@@ -33,6 +34,133 @@
 TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER'
 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" )
 
+def add_installation_directories_to_tool_dependencies( trans, repository_name, repository_owner, changeset_revision, tool_dependencies ):
+    for dependency_key, requirements_dict in tool_dependencies.items():
+        if dependency_key not in [ 'set_environment' ]:
+            dependency_name = requirements_dict[ 'name' ]
+            version = requirements_dict[ 'version' ]
+            type = requirements_dict[ 'type' ]
+            install_dir = os.path.join( trans.app.config.tool_dependency_dir,
+                                        dependency_name,
+                                        version,
+                                        repository_owner,
+                                        repository_name,
+                                        changeset_revision )
+            requirements_dict[ 'install_dir' ] = install_dir
+            tool_dependencies[ dependency_key ] = requirements_dict
+    return tool_dependencies
+def build_readme_files_dict( repository_metadata ):
+    """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata."""
+    readme_files_dict = {}
+    if repository_metadata:
+        metadata = repository_metadata.metadata
+        if metadata and 'readme_files' in metadata:
+            for relative_path_to_readme_file in metadata[ 'readme_files' ]:
+                readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
+                full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
+                try:
+                    f = open( full_path_to_readme_file, 'r' )
+                    text = f.read()
+                    f.close()
+                    readme_files_dict[ readme_file_name ] = str( text )
+                except Exception, e:
+                    log.debug( "Error reading README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \
+                               ( str( relative_path_to_readme_file ), str( repository_name ), str( changeset_revision ), str( e ) ) )
+    return readme_files_dict
+def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, 
+                                            readme_files_dict, repository_dependencies, tool_dependencies ):
+    """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy."""
+    containers_dict = dict( readme_files=None, repository_dependencies=None, tool_dependencies=None )
+    if readme_files_dict or repository_dependencies or tool_dependencies:
+        lock = threading.Lock()
+        lock.acquire( True )
+        if tool_dependencies:
+            # Add the install_dir attribute to the tool_dependencies.
+            tool_dependencies = add_installation_directories_to_tool_dependencies( trans, repository_name, repository_owner, changeset_revision, tool_dependencies )
+        try:
+            folder_id = 0
+            if readme_files_dict:
+                folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict )
+                containers_dict[ 'readme_files' ] = readme_files_root_folder
+            if repository_dependencies:
+                folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url,
+                                                                                                       repository_name=repository_name,
+                                                                                                       repository_owner=repository_owner,
+                                                                                                       changeset_revision=changeset_revision,
+                                                                                                       folder_id=folder_id,
+                                                                                                       repository_dependencies=repository_dependencies )
+                containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder
+            if tool_dependencies:
+                folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True )
+                containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder
+        except Exception, e:
+            log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) )
+        finally:
+            lock.release()
+    return containers_dict
+def build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata ):
+    """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed."""
+    containers_dict = dict( datatypes=None,
+                            invalid_tools=None,
+                            readme_files=None,
+                            repository_dependencies=None,
+                            tool_dependencies=None,
+                            valid_tools=None,
+                            workflows=None )
+    if repository_metadata:
+        metadata = repository_metadata.metadata
+        lock = threading.Lock()
+        lock.acquire( True )
+        try:
+            folder_id = 0
+            # Datatypes container.
+            if metadata and 'datatypes' in metadata:
+                datatypes = metadata[ 'datatypes' ]
+                folder_id, datatypes_root_folder = build_datatypes_folder( folder_id, datatypes )
+                containers_dict[ 'datatypes' ] = datatypes_root_folder
+            # Invalid tools container.
+            if metadata and 'invalid_tools' in metadata:
+                invalid_tool_configs = metadata[ 'invalid_tools' ]
+                folder_id, invalid_tools_root_folder = build_invalid_tools_folder( folder_id,
+                                                                                   invalid_tool_configs,
+                                                                                   changeset_revision,
+                                                                                   repository=repository,
+                                                                                   label='Invalid tools' )
+                containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder
+            # Readme files container.
+            readme_files_dict = build_readme_files_dict( repository_metadata )
+            folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict )
+            containers_dict[ 'readme_files' ] = readme_files_root_folder
+            # Repository dependencies container.
+            toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' )
+            folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url,
+                                                                                                   repository_name=repository.name,
+                                                                                                   repository_owner=repository.user.username,
+                                                                                                   changeset_revision=changeset_revision,
+                                                                                                   folder_id=folder_id,
+                                                                                                   repository_dependencies=repository_dependencies )
+            if repository_dependencies_root_folder:
+                containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder
+            # Tool dependencies container.
+            if metadata and 'tool_dependencies' in metadata:
+                tool_dependencies = metadata[ 'tool_dependencies' ]
+                folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=False )
+                containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder
+            # Valid tools container.
+            if metadata and 'tools' in metadata:
+                valid_tools = metadata[ 'tools' ]
+                folder_id, valid_tools_root_folder = build_tools_folder( folder_id, valid_tools, repository, changeset_revision, label='Valid tools' )
+                containers_dict[ 'valid_tools' ] = valid_tools_root_folder
+            # Workflows container.
+            if metadata and 'workflows' in metadata:
+                workflows = metadata[ 'workflows' ]
+                folder_id, workflows_root_folder = build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' )
+                containers_dict[ 'workflows' ] = workflows_root_folder
+        except Exception, e:
+            log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) )
+        finally:
+            lock.release()
+    return containers_dict
 def build_repository_ids_select_field( trans, cntrller, name='repository_ids', multiple=True, display='checkboxes' ):
     """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata."""
     repositories_select_field = SelectField( name=name, multiple=multiple, display=display )
@@ -336,14 +464,40 @@
     trans.sa_session.add( repository_metadata )
     trans.sa_session.flush()
     return repository_metadata
-def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ):
+def create_repo_info_dict( trans, repo, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
+                           repository=None, repository_metadata=None ):
+    """
+    Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance.  The dictionary will also contain
+    the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies.  This method is called during the
+    tool shed repository installation process from Galaxy.  In this case both the received repository and repository_metadata will be objects, but repository_name
+    sill be None.  This method is also called when a tool shed repository that was uninstalled from a Galaxy instance is being re-installed.  In this case, both
+    repository and repository_metadata will be None, but repository_name will have a value.
+    """
     repo_info_dict = {}
-    repo_info_dict[ repository.name ] = ( repository.description,
-                                          repository_clone_url,
-                                          changeset_revision,
-                                          ctx_rev,
-                                          owner,
-                                          metadata.get( 'tool_dependencies', None ) )
+    if repository is None and repository_metadata is None:
+        # The repository associated with the received repository_clone_url is being re-installed into a Galaxy instance, so we need to retrieve the
+        # appropriate repository from the tool shed using the received information.
+        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )
+    if repository_metadata:
+        metadata = repository_metadata.metadata
+        if metadata:
+            # Get a dictionary of all repositories upon which the contents of the received repository depends.
+            repository_dependencies = get_repository_dependencies_for_changeset_revision( trans,
+                                                                                          repo,
+                                                                                          repository,
+                                                                                          repository_metadata,
+                                                                                          str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                          repository_dependencies=None,
+                                                                                          all_repository_dependencies=None )
+            # Cast unicode to string.
+            repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
+                                                         str( repository_clone_url ),
+                                                         str( changeset_revision ),
+                                                         str( ctx_rev ),
+                                                         str( repository_owner ),
+                                                         repository_dependencies,
+                                                         metadata.get( 'tool_dependencies', None ) )
     return repo_info_dict
 def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
     """Generate the URL for cloning a repository that is in the tool shed."""
@@ -464,7 +618,8 @@
     else:
         original_repository_metadata = None
     readme_file_names = get_readme_file_names( repository.name )
-    metadata_dict = { 'shed_config_filename': shed_config_dict.get( 'config_filename' ) }
+    metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) }
+    readme_files = []
     invalid_file_tups = []
     invalid_tool_configs = []
     tool_dependencies_config = None
@@ -524,7 +679,7 @@
                                                                                                      shed_config_dict,
                                                                                                      resetting_all_metadata_on_repository )
                     metadata_dict = generate_repository_dependency_metadata( relative_path_to_repository_dependencies, metadata_dict )
-                # See if we have a READ_ME file.
+                # See if we have one or more READ_ME files.
                 elif name.lower() in readme_file_names:
                     relative_path_to_readme = get_relative_path_to_repository_file( root,
                                                                                     name,
@@ -532,7 +687,7 @@
                                                                                     work_dir,
                                                                                     shed_config_dict,
                                                                                     resetting_all_metadata_on_repository )
-                    metadata_dict[ 'readme' ] = relative_path_to_readme
+                    readme_files.append( relative_path_to_readme )
                 # See if we have a tool config.
                 elif name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ):
                     full_path = str( os.path.abspath( os.path.join( root, name ) ) )
@@ -583,6 +738,8 @@
                         exported_workflow_dict = from_json_string( workflow_text )
                         if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
                             metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
+    if readme_files:
+        metadata_dict[ 'readme_files' ] = readme_files
     if 'tools' in metadata_dict:
         # This step must be done after metadata for tools has been defined.
         tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir )
@@ -864,6 +1021,80 @@
         valid_filenames.append( '%s.txt' % r )
     valid_filenames.append( '%s.txt' % repository_name )
     return valid_filenames
+def get_repository_by_name_and_owner( trans, name, owner ):
+    """Get a repository from the database via name and owner"""
+    user = get_user_by_username( trans, owner )
+    return trans.sa_session.query( trans.model.Repository ) \
+                             .filter( and_( trans.model.Repository.table.c.name == name,
+                                            trans.model.Repository.table.c.user_id == user.id ) ) \
+                             .first()
+def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, repository_dependencies=None,
+                                                        all_repository_dependencies=None ):
+    """
+    Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend.  The dictionary keys
+    are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of
+    repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ).  This method
+    ensures that all required repositories to the nth degree are returned.
+    """
+    if all_repository_dependencies is None:
+        all_repository_dependencies = {}
+    if repository_dependencies is None:
+        repository_dependencies = []
+    metadata = repository_metadata.metadata
+    if metadata and 'repository_dependencies' in metadata:
+        repository_dependencies_root_key = generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url,
+                                                                                                repository_name=repository.name,
+                                                                                                repository_owner=repository.user.username,
+                                                                                                changeset_revision=repository_metadata.changeset_revision )
+        for repository_dependency in metadata[ 'repository_dependencies' ]:
+            if repository_dependency not in repository_dependencies:
+                repository_dependencies.append( repository_dependency )
+    else:
+        repository_dependencies_root_key = None
+    if repository_dependencies:
+        repository_dependency = repository_dependencies.pop( 0 )
+        # Cast unicode to string.
+        repository_dependency = [ str( item ) for item in repository_dependency ]
+        tool_shed, name, owner, changeset_revision = repository_dependency
+        if repository_dependencies_root_key:
+            if repository_dependencies_root_key in all_repository_dependencies:
+                # See if this repository_dependency is contained in the list associated with the repository_dependencies_root_key.
+                all_repository_dependencies_val = all_repository_dependencies[ repository_dependencies_root_key ]
+                if repository_dependency not in all_repository_dependencies_val:
+                    all_repository_dependencies_val.append( repository_dependency )
+                    all_repository_dependencies[ repository_dependencies_root_key ] = all_repository_dependencies_val
+            else:
+                # Insert this repository_dependency.
+                all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ]
+        if tool_shed_is_this_tool_shed( tool_shed ):
+            # The repository is in the current tool shed.
+            required_repository = get_repository_by_name_and_owner( trans, name, owner )
+            required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
+                                                                                                       trans.security.encode_id( required_repository.id ),
+                                                                                                       changeset_revision )
+            if required_repository_metadata:
+                required_repo_dir = required_repository.repo_path( trans.app )
+                required_repo = hg.repository( get_configured_ui(), required_repo_dir )
+            else:
+                # The repository changeset_revision is no longer installable, so see if there's been an update.
+                required_repo_dir = required_repository.repo_path( trans.app )
+                required_repo = hg.repository( get_configured_ui(), required_repo_dir )
+                required_repository_metadata = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision )
+            if required_repository_metadata:
+                # The required_repository_metadata changeset_revision is installable.
+                required_metadata = required_repository_metadata.metadata
+                if required_metadata:
+                    return get_repository_dependencies_for_changeset_revision( trans=trans,
+                                                                               repo=required_repo,
+                                                                               repository=required_repository,
+                                                                               repository_metadata=required_repository_metadata,
+                                                                               toolshed_base_url=tool_shed,
+                                                                               repository_dependencies=repository_dependencies,
+                                                                               all_repository_dependencies=all_repository_dependencies )     
+        else:
+            # The repository is in a different tool shed, so build an url and send a request.
+            raise Exception( "Repository dependencies that refer to repositories in other tool sheds is not yet supported." )
+    return all_repository_dependencies
 def get_repository_file_contents( file_path ):
     if is_gzip( file_path ):
         to_html = to_html_str( '\ngzip compressed file\n' )
@@ -917,6 +1148,12 @@
     elif all_metadata_records:
         return all_metadata_records[ 0 ]
     return None
+def get_repository_metadata_by_repository_id_changset_revision( trans, id, changeset_revision ):
+    """Get a specified metadata record for a specified repository."""
+    return trans.sa_session.query( trans.model.RepositoryMetadata ) \
+                           .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ),
+                                          trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
+                           .first()
 def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ):
     if resetting_all_metadata_on_repository:
         full_path_to_file = os.path.join( root, name )
@@ -959,6 +1196,11 @@
                                     relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
                         sample_file_metadata_paths.append( relative_path_to_sample_file )
     return sample_file_metadata_paths, sample_file_copy_paths
+def get_user_by_username( trans, username ):
+    """Get a user from the database by username"""
+    return trans.sa_session.query( trans.model.User ) \
+                           .filter( trans.model.User.table.c.username == username ) \
+                           .one()
 def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ):
     """
     This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an
@@ -1348,6 +1590,8 @@
         elif c not in [ '\r' ]:
             translated.append( '' )
     return ''.join( translated )
+def tool_shed_is_this_tool_shed( toolshed_base_url ):
+    return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
 def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ):
     """
     Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates 


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -1,4 +1,4 @@
-import os, string, socket, logging, simplejson, binascii, tempfile, filecmp, threading
+import os, string, socket, logging, simplejson, binascii, tempfile, filecmp
 from time import strftime
 from datetime import *
 from galaxy.datatypes.checkers import *
@@ -7,7 +7,6 @@
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.hash_util import *
 from galaxy.util.shed_util_common import *
-from galaxy.webapps.community.util.container_util import *
 from galaxy.web.base.controller import *
 from galaxy.web.base.controllers.admin import *
 from galaxy.webapps.community import model
@@ -21,11 +20,11 @@
 log = logging.getLogger( __name__ )
 
 new_repo_email_alert_template = """
+Repository name:       ${repository_name}
 Revision:              ${revision}
 Change description:
 ${description}
 
-Repository name:       ${repository_name}
 Uploaded by:           ${username}
 Date content uploaded: ${display_date}
 
@@ -41,24 +40,23 @@
 """
 
 email_alert_template = """
-GALAXY TOOL SHED REPOSITORY UPDATE ALERT
------------------------------------------------------------------------------
-You received this alert because you registered to receive email whenever
-changes were made to the repository named "${repository_name}".
------------------------------------------------------------------------------
-
-Date of change: ${display_date}
-Changed by:     ${username}
-
+Repository name:       ${repository_name}
 Revision: ${revision}
 Change description:
 ${description}
 
+Changed by:     ${username}
+Date of change: ${display_date}
+
 ${content_alert_str}
 
 -----------------------------------------------------------------------------
 This change alert was sent from the Galaxy tool shed hosted on the server
 "${host}"
+-----------------------------------------------------------------------------
+You received this alert because you registered to receive email whenever
+changes were made to the repository named "${repository_name}".
+-----------------------------------------------------------------------------
 """
 
 contact_owner_template = """
@@ -104,62 +102,6 @@
             trans.sa_session.flush()
         return item_rating
 
-def build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata ):
-    containers_dict = dict( datatypes=None,
-                            invalid_tools=None,
-                            repository_dependencies=None,
-                            tool_dependencies=None,
-                            valid_tools=None,
-                            workflows=None )
-    if repository_metadata:
-        metadata = repository_metadata.metadata
-        lock = threading.Lock()
-        lock.acquire( True )
-        try:
-            folder_id = 0
-            # Datatypes container.
-            if metadata and 'datatypes' in metadata:
-                datatypes = metadata[ 'datatypes' ]
-                folder_id, datatypes_root_folder = build_datatypes_folder( folder_id, datatypes )
-                containers_dict[ 'datatypes' ] = datatypes_root_folder
-            # Invalid tools container.
-            if metadata and 'invalid_tools' in metadata:
-                invalid_tool_configs = metadata[ 'invalid_tools' ]
-                folder_id, invalid_tools_root_folder = build_invalid_tools_folder( folder_id,
-                                                                                   invalid_tool_configs,
-                                                                                   repository,
-                                                                                   changeset_revision,
-                                                                                   label='Invalid tools' )
-                containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder
-            # Repository dependencies container.
-            folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( repository,
-                                                                                                   changeset_revision,
-                                                                                                   folder_id,
-                                                                                                   repository_dependencies )
-            if repository_dependencies_root_folder:
-                containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder
-            # Tool dependencies container.
-            if metadata and 'tool_dependencies' in metadata:
-                tool_dependencies = metadata[ 'tool_dependencies' ]
-                folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies )
-                containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder
-            # Valid tools container.
-            if metadata and 'tools' in metadata:
-                valid_tools = metadata[ 'tools' ]
-                folder_id, valid_tools_root_folder = build_tools_folder( folder_id, valid_tools, repository, changeset_revision, label='Valid tools' )
-                containers_dict[ 'valid_tools' ] = valid_tools_root_folder
-            # Workflows container.
-            if metadata and 'workflows' in metadata:
-                workflows = metadata[ 'workflows' ]
-                folder_id, workflows_root_folder = build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' )
-                containers_dict[ 'workflows' ] = workflows_root_folder
-        except Exception, e:
-            repository_dependencies_root_folder = None
-            tool_dependencies_root_folder  = None
-            log.debug( "Exception in build_repository_containers: %s" % str( e ) )
-        finally:
-            lock.release()
-    return containers_dict
 def add_tool_versions( trans, id, repository_metadata, changeset_revisions ):
     # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata.
     metadata = repository_metadata.metadata
@@ -401,75 +343,6 @@
 def get_repository_by_name( trans, name ):
     """Get a repository from the database via name"""
     return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one()
-def get_repository_by_name_and_owner( trans, name, owner ):
-    """Get a repository from the database via name and owner"""
-    user = get_user_by_username( trans, owner )
-    return trans.sa_session.query( trans.model.Repository ) \
-                             .filter( and_( trans.model.Repository.table.c.name == name,
-                                            trans.model.Repository.table.c.user_id == user.id ) ) \
-                             .first()
-def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, repository_dependencies=None,
-                                                        all_repository_dependencies=None ):
-    """
-    Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend.  The dictionary keys
-    are name-spaced values consisting of tool_shed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of
-    repository_dependency tuples consisting of ( tool_shed_base_url, repository_name, repository_owner, changeset_revision ).  This is a
-    recursive method, so it ensures that all required repositories to the nth degree are returned.
-    """   
-    if all_repository_dependencies is None:
-        all_repository_dependencies = odict()
-    if repository_dependencies is None:
-        repository_dependencies = []
-    metadata = repository_metadata.metadata
-    if metadata and 'repository_dependencies' in metadata:
-        repository_dependencies_root_key = generate_repository_dependencies_key_for_repository( repository, repository_metadata.changeset_revision )
-        for repository_dependency in metadata[ 'repository_dependencies' ]:
-            if repository_dependency not in repository_dependencies:
-                repository_dependencies.append( repository_dependency )
-    else:
-        repository_dependencies_root_key = None
-    if repository_dependencies:
-        repository_dependency = repository_dependencies.pop( 0 )
-        tool_shed, name, owner, changeset_revision = repository_dependency
-        if repository_dependencies_root_key:
-            if repository_dependencies_root_key in all_repository_dependencies:
-                # See if this repository_dependency is contained in the list associated with the repository_dependencies_root_key.
-                all_repository_dependencies_val = all_repository_dependencies[ repository_dependencies_root_key ]
-                if repository_dependency not in all_repository_dependencies_val:
-                    all_repository_dependencies_val.append( repository_dependency )
-                    all_repository_dependencies[ repository_dependencies_root_key ] = all_repository_dependencies_val
-            else:
-                # Insert this repository_dependency.
-                all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ]
-        if tool_shed_is_this_tool_shed( tool_shed ):
-            # The repository is in the current tool shed.
-            required_repository = get_repository_by_name_and_owner( trans, name, owner )
-            required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
-                                                                                                       trans.security.encode_id( required_repository.id ),
-                                                                                                       changeset_revision )
-            if required_repository_metadata:
-                required_repo_dir = required_repository.repo_path( trans.app )
-                required_repo = hg.repository( get_configured_ui(), required_repo_dir )
-            else:
-                # The repository changeset_revision is no longer installable, so see if there's been an update.
-                required_repo_dir = required_repository.repo_path( trans.app )
-                required_repo = hg.repository( get_configured_ui(), required_repo_dir )
-                required_repository_metadata = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision )
-            if required_repository_metadata:
-                # The required_repository_metadata changeset_revision is installable.
-                required_metadata = required_repository_metadata.metadata
-                if required_metadata:
-                    return get_repository_dependencies_for_changeset_revision( trans=trans,
-                                                                               repo=required_repo,
-                                                                               repository=required_repository,
-                                                                               repository_metadata=required_repository_metadata,
-                                                                               toolshed_base_url=tool_shed,
-                                                                               repository_dependencies=repository_dependencies,
-                                                                               all_repository_dependencies=all_repository_dependencies )     
-        else:
-            # The repository is in a different tool shed, so build an url and send a request.
-            raise Exception( "Repository dependencies that refer to repositories in other tool sheds is not yet supported." )
-    return all_repository_dependencies
 def get_repository_metadata_by_id( trans, id ):
     """Get repository metadata from the database"""
     return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) )
@@ -477,12 +350,6 @@
     """Get all metadata records for a specified repository."""
     return trans.sa_session.query( trans.model.RepositoryMetadata ) \
                            .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) )
-def get_repository_metadata_by_repository_id_changset_revision( trans, id, changeset_revision ):
-    """Get a specified metadata record for a specified repository."""
-    return trans.sa_session.query( trans.model.RepositoryMetadata ) \
-                           .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ),
-                                          trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
-                           .first()
 def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
     repository_metadata_revisions = []
     metadata_changeset_revision_hashes = []
@@ -635,7 +502,7 @@
                 else:
                     email_alerts.append( user.email )
         else:
-            subject = "Galaxy tool shed repository update alert"
+            subject = "Galaxy tool shed update alert for repository named %s" % str( repository.name )
             email_alerts = from_json_string( repository.email_alerts )
         for email in email_alerts:
             to = email.strip()
@@ -827,8 +694,6 @@
                                                           id=trans.security.encode_id( repository.id ),
                                                           message=error_message,
                                                           status='error' ) )
-def tool_shed_is_this_tool_shed( toolshed_base_url ):
-    return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
 def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
     # This method id deprecated, but we'll keep it around for a while in case we need it.  The problem is that hg purge
     # is not supported by the mercurial API.


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/webapps/community/controllers/hg.py
--- a/lib/galaxy/webapps/community/controllers/hg.py
+++ b/lib/galaxy/webapps/community/controllers/hg.py
@@ -1,6 +1,7 @@
 import os, logging
 from galaxy.web.base.controller import *
-from galaxy.webapps.community.controllers.common import *
+from galaxy.util.shed_util_common import get_repository_by_name_and_owner
+from galaxy.webapps.community.controllers.common import set_repository_metadata
 
 from galaxy import eggs
 eggs.require('mercurial')


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1278,6 +1278,7 @@
         it into a local Galaxy instance.
         """
         includes_tools = False
+        includes_repository_dependencies = False
         includes_tool_dependencies = False
         repo_info_dicts = []
         for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
@@ -1288,33 +1289,39 @@
             metadata = repository_metadata.metadata
             if not includes_tools and 'tools' in metadata:
                 includes_tools = True
+            if not includes_repository_dependencies and 'repository_dependencies' in metadata:
+                includes_repository_dependencies = True
             if not includes_tool_dependencies and 'tool_dependencies' in metadata:
                 includes_tool_dependencies = True
             repo_dir = repository.repo_path( trans.app )
             repo = hg.repository( get_configured_ui(), repo_dir )
             ctx = get_changectx_for_changeset( repo, changeset_revision )
-            repo_info_dict = create_repo_info_dict( repository, repository.user.username, repository_clone_url, changeset_revision, str( ctx.rev() ), metadata )
+            repo_info_dict = create_repo_info_dict( trans=trans,
+                                                    repo=repo,
+                                                    repository_clone_url=repository_clone_url,
+                                                    changeset_revision=changeset_revision,
+                                                    ctx_rev=str( ctx.rev() ),
+                                                    repository_owner=repository.user.username,
+                                                    repository_name=None,
+                                                    repository=repository,
+                                                    repository_metadata=repository_metadata )      
             repo_info_dicts.append( tool_shed_encode( repo_info_dict ) )
-        return dict( includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts )
-    @web.expose
-    def get_readme( self, trans, **kwd ):
-        """If the received changeset_revision includes a readme file, return it's contents."""
+        return dict( includes_tools=includes_tools,
+                     includes_repository_dependencies=includes_repository_dependencies,
+                     includes_tool_dependencies=includes_tool_dependencies,
+                     repo_info_dicts=repo_info_dicts )
+    @web.json
+    def get_readme_files( self, trans, **kwd ):
+        """
+        This method is called when installing or re-installing a single repository into a Galaxy instance.  If the received changeset_revision 
+        includes one or more readme files, return them in a dictionary.
+        """
         repository_name = kwd[ 'name' ]
         repository_owner = kwd[ 'owner' ]
         changeset_revision = kwd[ 'changeset_revision' ]
         repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )
-        metadata = repository_metadata.metadata
-        if metadata and 'readme' in metadata:
-            try:
-                f = open( metadata[ 'readme' ], 'r' )
-                text = f.read()
-                f.close()
-                return str( text )
-            except Exception, e:
-                log.debug( "Error attempting to read README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \
-                           ( str( metadata[ 'readme' ] ), str( repository_name ), str( changeset_revision ), str( e ) ) )
-        return ''
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )        
+        return build_readme_files_dict( repository_metadata )
     @web.expose
     def get_tool_dependencies( self, trans, **kwd ):
         """Handle a request from a local Galaxy instance."""
@@ -1799,7 +1806,7 @@
             review_id = trans.security.encode_id( review.id )
         else:
             review_id = None
-        containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/manage_repository.mako',
                                     cntrller=cntrller,
                                     repo_name=repo_name,
@@ -1867,8 +1874,6 @@
         return state
     @web.json
     def open_folder( self, trans, folder_path ):
-        # The tool shed includes a repository source file browser, which currently depends upon
-        # copies of the hg repository file store in the repo_path for browsing.
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
@@ -1904,7 +1909,7 @@
                                                                                  selected_value=changeset_revision,
                                                                                  add_id_to_name=False,
                                                                                  downloadable=False )
-        containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
                                     repository=repository,
                                     containers_dict=containers_dict,
@@ -2373,52 +2378,6 @@
                                                               action='view_repository',
                                                               **kwd ) )
     @web.expose
-    def view_readme( self, trans, id, changeset_revision, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository_in_tool_shed( trans, id )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )
-        if repository_metadata:
-            metadata = repository_metadata.metadata
-        else:
-            metadata = None
-        if metadata and 'readme' in metadata:
-            readme_file = str( metadata[ 'readme' ] )
-            repo_files_dir = repository.repo_path( trans.app )
-            try:
-                f = open( readme_file, 'r' )
-                raw_text = f.read()
-                f.close()
-            except IOError:
-                work_dir = tempfile.mkdtemp()
-                try:
-                    manifest_readme_file = self.get_file_from_changeset_revision( repo_files_dir, changeset_revision, readme_file, work_dir )
-                    f = open( manifest_readme_file, 'r' )
-                    raw_text = f.read()
-                    f.close()
-                    remove_dir( work_dir )
-                except Exception, e:
-                    raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) )
-                    log.debug( raw_text )
-                    remove_dir( work_dir )
-            except Exception, e:
-                raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) )
-                log.debug( raw_text )
-            readme_text = raw_text
-        else:
-            readme_text = ''
-        is_malicious = changeset_is_malicious( trans, id, changeset_revision )
-        return trans.fill_template( '/webapps/community/common/view_readme.mako',
-                                    cntrller=cntrller,
-                                    repository=repository,
-                                    changeset_revision=changeset_revision,
-                                    readme_text=readme_text,
-                                    is_malicious=is_malicious,
-                                    message=message,
-                                    status=status )
-    @web.expose
     def view_repository( self, trans, id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
@@ -2492,7 +2451,7 @@
             review_id = trans.security.encode_id( review.id )
         else:
             review_id = None
-        containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/view_repository.mako',
                                     cntrller=cntrller,
                                     repo=repo,


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/webapps/community/util/container_util.py
--- a/lib/galaxy/webapps/community/util/container_util.py
+++ b/lib/galaxy/webapps/community/util/container_util.py
@@ -1,4 +1,4 @@
-import logging
+import os, logging
 from galaxy.web import url_for
 
 log = logging.getLogger( __name__ )
@@ -18,6 +18,7 @@
         self.valid_tools = []
         self.tool_dependencies = []
         self.repository_dependencies = []
+        self.readme_files = []
         self.workflows = []
     def contains_folder( self, folder ):
         for index, contained_folder in enumerate( self.folders ):
@@ -42,6 +43,13 @@
         self.repository_id = repository_id
         self.changeset_revision = changeset_revision
 
+class ReadMe( object ):
+    """Readme text object"""
+    def __init__( self, id=None, name=None, text=None ):
+        self.id = id
+        self.name = name
+        self.text = text
+
 class RepositoryDependency( object ):
     """Repository dependency object"""
     def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None ):
@@ -67,11 +75,13 @@
 
 class ToolDependency( object ):
     """Tool dependency object"""
-    def __init__( self, id=None, name=None, version=None, type=None ):
+    def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None ):
         self.id = id
         self.name = name
         self.version = version
         self.type = type
+        self.install_dir = install_dir
+        self.readme = readme
 
 class Workflow( object ):
     """Workflow object"""
@@ -111,8 +121,9 @@
     else:
         datatypes_root_folder = None
     return folder_id, datatypes_root_folder
-def build_invalid_tools_folder( folder_id, invalid_tool_configs, repository, changeset_revision, label='Invalid tools' ):
+def build_invalid_tools_folder( folder_id, invalid_tool_configs, changeset_revision, repository=None, label='Invalid tools' ):
     """Return a folder hierarchy containing invalid tools."""
+    # TODO: Should we display invalid tools on the tool panel selection page when installing the repository into Galaxy?
     if invalid_tool_configs:
         invalid_tool_id = 0
         folder_id += 1
@@ -122,15 +133,41 @@
         invalid_tools_root_folder.folders.append( folder )
         for invalid_tool_config in invalid_tool_configs:
             invalid_tool_id += 1
+            if repository:
+                repository_id = repository.id
+            else:
+                repository_id = None
             invalid_tool = InvalidTool( id=invalid_tool_id,
                                         tool_config=invalid_tool_config,
-                                        repository_id=repository.id,
+                                        repository_id=repository_id,
                                         changeset_revision=changeset_revision )
             folder.invalid_tools.append( invalid_tool )
     else:
         invalid_tools_root_folder = None
     return folder_id, invalid_tools_root_folder
-def build_repository_dependencies_folder( repository, changeset_revision, folder_id, repository_dependencies, label='Repository dependencies' ):
+def build_readme_files_folder( folder_id, readme_files_dict, label='Readme files' ):
+    """Return a folder hierarchy containing readme text files."""
+    if readme_files_dict:
+        readme_id = 0
+        folder_id += 1
+        readme_files_root_folder = Folder( id=folder_id, key='root', label='root' )
+        folder_id += 1
+        readme_files_folder = Folder( id=folder_id, key='readme_files', label=label )
+        readme_files_root_folder.folders.append( readme_files_folder )
+        for readme_file_name, readme_file_text in readme_files_dict.items():
+            readme_id += 1
+            readme = ReadMe( id=readme_id,
+                             name=readme_file_name,
+                             text=readme_file_text )
+            folder_id += 1
+            folder = Folder( id=folder_id, key=readme.name, label=readme.name )
+            folder.readme_files.append( readme )
+            readme_files_folder.folders.append( folder )
+    else:
+        readme_files_root_folder = None
+    return folder_id, readme_files_root_folder
+def build_repository_dependencies_folder( toolshed_base_url, repository_name, repository_owner, changeset_revision, folder_id, repository_dependencies,
+                                          label='Repository dependencies' ):
     """Return a folder hierarchy containing repository dependencies."""
     if repository_dependencies:
         repository_dependency_id = 0
@@ -139,7 +176,7 @@
         repository_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' )
         folder_id += 1
         # Create the Repository dependencies folder and add it to the root folder.
-        key = generate_repository_dependencies_key_for_repository( repository, changeset_revision )
+        key = generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision )
         repository_dependencies_folder = Folder( id=folder_id, key=key, label=label )
         repository_dependencies_root_folder.folders.append( repository_dependencies_folder )
         # Process the repository dependencies.
@@ -149,7 +186,7 @@
             if not folder:
                 # Create a new folder.
                 folder_id += 1
-                label = generate_repository_dependencies_folder_label_from_key( repository, changeset_revision, key )
+                label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key )
                 folder = Folder( id=folder_id, key=key, label=label )
             for repository_dependency_tup in val:
                 toolshed, name, owner, changeset_revision = repository_dependency_tup
@@ -213,7 +250,7 @@
     else:
         tools_root_folder = None
     return folder_id, tools_root_folder
-def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Tool dependencies' ):
+def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Tool dependencies', for_galaxy=False ):
     """Return a folder hierarchy containing tool dependencies."""
     if tool_dependencies:
         tool_dependency_id = 0
@@ -224,22 +261,40 @@
         tool_dependencies_root_folder.folders.append( folder )
         # Insert a header row.
         tool_dependency_id += 1
-        tool_dependency = ToolDependency( id=tool_dependency_id,
-                                          name='Name',
-                                          version='Version',
-                                          type='Type' )
+        if for_galaxy:
+            # Include the installation directory.
+            tool_dependency = ToolDependency( id=tool_dependency_id,
+                                              name='Name',
+                                              version='Version',
+                                              type='Type',
+                                              install_dir='Install directory' )
+        else:
+            tool_dependency = ToolDependency( id=tool_dependency_id,
+                                              name='Name',
+                                              version='Version',
+                                              type='Type' )
         folder.tool_dependencies.append( tool_dependency )
         for dependency_key, requirements_dict in tool_dependencies.items():
             tool_dependency_id += 1
             if dependency_key == 'set_environment':
-                version = None
+                for set_environment_dict in requirements_dict:
+                    name = set_environment_dict[ 'name' ]
+                    type = set_environment_dict[ 'type' ]
+                    tool_dependency = ToolDependency( id=tool_dependency_id,
+                                                      name=name,
+                                                      type=type )
+                    folder.tool_dependencies.append( tool_dependency )
             else:
+                name = requirements_dict[ 'name' ]
                 version = requirements_dict[ 'version' ]
-            tool_dependency = ToolDependency( id=tool_dependency_id,
-                                              name=requirements_dict[ 'name' ],
-                                              version=version,
-                                              type=requirements_dict[ 'type' ] )
-            folder.tool_dependencies.append( tool_dependency )
+                type = requirements_dict[ 'type' ]
+                install_dir = requirements_dict.get( 'install_dir', None )
+                tool_dependency = ToolDependency( id=tool_dependency_id,
+                                                  name=name,
+                                                  version=version,
+                                                  type=type,
+                                                  install_dir=install_dir )
+                folder.tool_dependencies.append( tool_dependency )
     else:
         tool_dependencies_root_folder = None
     return folder_id, tool_dependencies_root_folder
@@ -279,18 +334,23 @@
     else:
         workflows_root_folder = None
     return folder_id, workflows_root_folder
-def generate_repository_dependencies_folder_label_from_key( repository, changeset_revision, key ):
+def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ):
     """Return a repository dependency label based on the repository dependency key."""
-    if key_is_current_repositorys_key( repository, changeset_revision, key ):
+    if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ):
         label = 'Repository dependencies'
     else:
         toolshed_base_url, name, owner, revision = get_components_from_key( key )
         label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, revision, owner )
     return label
-def generate_repository_dependencies_key_for_repository( repository, changeset_revision ):
+def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision ):
     # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported.
-    toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' )
-    return '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository.name, STRSEP, repository.user.username, STRSEP, changeset_revision )
+    return '%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ),
+                                STRSEP,
+                                str( repository_name ),
+                                STRSEP,
+                                str( repository_owner ),
+                                STRSEP,
+                                str( changeset_revision ) )
 def get_folder( folder, key ):
     if folder and folder.key == key:
         return folder
@@ -308,7 +368,7 @@
 def is_folder( folder_keys, toolshed_base_url, repository_name, repository_owner, changeset_revision ):
     key = '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision )
     return key in folder_keys
-def key_is_current_repositorys_key( repository, changeset_revision, key ):
-    toolshed_base_url, repository_name, repository_owner, changeset_revision = get_components_from_key( key )
-    return repository_name == repository.name and repository_owner == repository.user.username and repository_changeset_revision == changeset_revision
+def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ):
+    toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key )
+    return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision
     
\ No newline at end of file


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -2,7 +2,6 @@
 from admin import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
-from galaxy.util.shed_util_common import *
 from galaxy.tool_shed.encoding_util import *
 from galaxy import eggs, tools
 
@@ -961,12 +960,6 @@
                                 url_args=dict( controller='admin_toolshed', 
                                                action='deactivate_or_uninstall_repository', 
                                                id=trans.security.encode_id( tool_shed_repository.id ) ) ) ]
-        if tool_shed_repository.metadata and 'readme' in tool_shed_repository.metadata:
-            view_readme_action = grids.GridAction( label='View README', 
-                                                   url_args=dict( controller='admin_toolshed', 
-                                                                  action='view_readme', 
-                                                                  id=trans.security.encode_id( tool_shed_repository.id ) ) )
-            self.tool_dependency_grid.global_actions.insert( 1, view_readme_action )
         if 'operation' in kwd:
             operation = kwd[ 'operation' ].lower()
             if not tool_dependency_ids:
@@ -1050,6 +1043,9 @@
         status = kwd.get( 'status', 'done' )
         includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
         tool_shed_url = kwd[ 'tool_shed_url' ]
+        # Handle repository dependencies.
+        includes_repository_dependencies = util.string_as_bool( kwd.get( 'includes_repository_dependencies', False ) )
+        install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' )
         # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
         new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
         tool_panel_section = kwd.get( 'tool_panel_section', '' )
@@ -1071,10 +1067,13 @@
             response.close()
             repo_information_dict = from_json_string( raw_text )
             includes_tools = util.string_as_bool( repo_information_dict[ 'includes_tools' ] )
+            includes_repository_dependencies = util.string_as_bool( repo_information_dict[ 'includes_repository_dependencies' ] )
             includes_tool_dependencies = util.string_as_bool( repo_information_dict[ 'includes_tool_dependencies' ] )
             encoded_repo_info_dicts = util.listify( repo_information_dict[ 'repo_info_dicts' ] )
         repo_info_dicts = [ tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
-        if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ):
+        if ( not includes_tools and not includes_repository_dependencies ) or \
+            ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ):
+            install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
             if includes_tools:
                 install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
                 shed_tool_conf = kwd[ 'shed_tool_conf' ]
@@ -1100,10 +1099,9 @@
             filtered_repo_info_dicts = []
             for repo_info_dict in repo_info_dicts:
                 for name, repo_info_tuple in repo_info_dict.items():
-                    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+                    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
                     clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) )
                     relative_install_dir = os.path.join( clone_dir, name )
-                    owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
                     # Make sure the repository was not already installed.
                     installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans,
                                                                                                                              tool_shed_url,
@@ -1111,7 +1109,7 @@
                                                                                                                              repo_info_tuple,
                                                                                                                              clone_dir )
                     if installed_tool_shed_repository:
-                        message += "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision )
+                        message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner )
                         if installed_changeset_revision != changeset_revision:
                             message += "was previously installed using changeset revision <b>%s</b>.  " % installed_changeset_revision
                         else:
@@ -1123,7 +1121,8 @@
                         if installed_changeset_revision != changeset_revision:
                             message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
                             message += "<b>Repository Actions</b> pop-up menu.  "
-                        message+= 'Click <a href="%s">here</a> to manage the repository.  ' % ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) )
+                        message+= 'Click <a href="%s">here</a> to manage the repository.  ' % \
+                            ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) )
                         status = 'error'
                         if len( repo_info_dicts ) == 1:
                             new_kwd = dict( message=message, status=status )
@@ -1131,7 +1130,7 @@
                                                                               action='browse_repositories',
                                                                               **new_kwd ) )
                     else:
-                        print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
+                        log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name )
                         tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app,
                                                                                       name=name,
                                                                                       description=description,
@@ -1141,7 +1140,7 @@
                                                                                       metadata_dict={},
                                                                                       status=trans.model.ToolShedRepository.installation_status.NEW,
                                                                                       current_changeset_revision=changeset_revision,
-                                                                                      owner=owner,
+                                                                                      owner=repository_owner,
                                                                                       dist_to_shed=False )
                         created_or_updated_tool_shed_repositories.append( tool_shed_repository )
                         filtered_repo_info_dicts.append( tool_shed_encode( repo_info_dict ) )
@@ -1171,6 +1170,7 @@
                     tool_section = None
                 tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ]
                 new_kwd = dict( includes_tools=includes_tools,
+                                includes_repository_dependencies=includes_repository_dependencies,
                                 includes_tool_dependencies=includes_tool_dependencies,
                                 install_tool_dependencies=install_tool_dependencies,
                                 message=message,
@@ -1203,42 +1203,53 @@
             shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
             shed_tool_conf_select_field = None
         tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
-        if includes_tools and len( repo_info_dicts ) == 1:
-            # If we're installing a single repository, see if it contains a readme file tha twe can display.
+        if len( repo_info_dicts ) == 1:
+            # If we're installing a single repository, see if it contains a readme or dependencies that we can display.
             repo_info_dict = repo_info_dicts[ 0 ]
             name = repo_info_dict.keys()[ 0 ]
             repo_info_tuple = repo_info_dict[ name ]
-            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
             url = url_join( tool_shed_url,
-                            'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \
+                            'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
                             ( name, repository_owner, changeset_revision ) )
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
-            readme_text = raw_text
+            readme_files_dict = from_json_string( raw_text )
+            containers_dict = build_repository_containers_for_galaxy( trans=trans,
+                                                                      toolshed_base_url=tool_shed_url,
+                                                                      repository_name=name,
+                                                                      repository_owner=repository_owner,
+                                                                      changeset_revision=changeset_revision,
+                                                                      readme_files_dict=readme_files_dict,
+                                                                      repository_dependencies=repository_dependencies,
+                                                                      tool_dependencies=tool_dependencies )
         else:
-            readme_text = '' 
+            containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
+        # Handle tool dependencies chack box.
         if trans.app.config.tool_dependency_dir is None:
             if includes_tool_dependencies:
-                message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b>"
-                message += " setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
+                message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
+                message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
                 status = "warning"
-            checked = False
+            install_tool_dependencies_check_box_checked = False
         else:
-            checked = True
-        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=checked )
+            install_tool_dependencies_check_box_checked = True
+        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
+        # Handle repository dependencies check box.
+        install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
         return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
                                     encoded_repo_info_dicts=encoded_repo_info_dicts,
                                     includes_tools=includes_tools,
                                     includes_tool_dependencies=includes_tool_dependencies,
+                                    install_repository_dependencies_check_box=install_repository_dependencies_check_box,
                                     install_tool_dependencies_check_box=install_tool_dependencies_check_box,
                                     new_tool_panel_section=new_tool_panel_section,
-                                    repo_info_dicts=repo_info_dicts,
+                                    containers_dict=containers_dict,
                                     shed_tool_conf=shed_tool_conf,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
                                     tool_shed_url=kwd[ 'tool_shed_url' ],
-                                    readme_text=readme_text,
                                     message=message,
                                     status=status )
     @web.expose
@@ -1269,8 +1280,8 @@
                     tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] )
             else:
                 tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] )
-            # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection.  The
-            # following assumes everything was loaded into 1 section (or no section) in the tool panel.
+            # Fix this to handle the case where the tools are distributed across in more than 1 ToolSection - this assumes everything was loaded into 1
+            # section (or no section) in the tool panel.
             tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ]
             tool_section_dict = tool_section_dicts[ 0 ]
             original_section_id = tool_section_dict[ 'id' ]
@@ -1328,12 +1339,16 @@
         # The repo_info_dict should be encoded.
         if not repo_info_dict:
             # This should only happen if the tool_shed_repository does not include any valid tools.
-            repo_info_dict = create_repo_info_dict( tool_shed_repository,
-                                                    tool_shed_repository.owner,
-                                                    repository_clone_url,
-                                                    tool_shed_repository.installed_changeset_revision,
-                                                    ctx_rev,
-                                                    metadata )
+            repo = hg.repository( get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) )
+            repo_info_dict = create_repo_info_dict( trans=trans,
+                                                    repo=repo,
+                                                    repository_clone_url=repository_clone_url,
+                                                    changeset_revision=tool_shed_repository.installed_changeset_revision,
+                                                    ctx_rev=ctx_rev,
+                                                    repository_owner=tool_shed_repository.owner,
+                                                    repository_name=tool_shed_repository.name,
+                                                    repository=None,
+                                                    repository_metadata=None )
             repo_info_dict = tool_shed_encode( repo_info_dict )
         new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies,
                         includes_tools=tool_shed_repository.includes_tools,
@@ -1410,12 +1425,16 @@
         tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision )
         repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
-        repo_info_dict = create_repo_info_dict( repository,
-                                                repository.owner,
-                                                repository_clone_url,
-                                                repository.installed_changeset_revision,
-                                                ctx_rev,
-                                                metadata )
+        repo = hg.repository( get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) )
+        repo_info_dict = create_repo_info_dict( trans=trans,
+                                                repo=repo,
+                                                repository_clone_url=repository_clone_url,
+                                                changeset_revision=repository.installed_changeset_revision,
+                                                ctx_rev=ctx_rev,
+                                                repository_owner=repository.owner,
+                                                repository_name=repository.name,
+                                                repository=None,
+                                                repository_metadata=None )
         # Get the location in the tool panel in which the tool was originally loaded.
         if 'tool_panel_section' in metadata:
             tool_panel_dict = metadata[ 'tool_panel_section' ]
@@ -1444,28 +1463,46 @@
             message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections.  " % repository.name
             message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section."
             status = 'warning'
-        includes_tool_dependencies = 'tool_dependencies' in metadata
-        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
-        if metadata and 'readme' in metadata:
+        if metadata and 'readme_files' in metadata:
             url = url_join( tool_shed_url,
-                            'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \
+                            'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
                             ( repository.name, repository.owner, repository.installed_changeset_revision ) )
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
-            readme_text = raw_text
+            readme_files_dict = from_json_string( raw_text )
+            containers_dict = build_repository_containers_for_galaxy( trans=trans,
+                                                                      toolshed_base_url=tool_shed_url,
+                                                                      repository_name=name,
+                                                                      repository_owner=repository_owner,
+                                                                      changeset_revision=changeset_revision,
+                                                                      readme_files_dict=readme_files_dict,
+                                                                      repository_dependencies=repository_dependencies,
+                                                                      tool_dependencies=tool_dependencies )
         else:
-            readme_text = '' 
+            containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
+        # Handle repository dependencies check box.
+        install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
+        # Handle tool dependencies check box.
+        if trans.app.config.tool_dependency_dir is None:
+            if includes_tool_dependencies:
+                message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
+                message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
+                status = "warning"
+            install_tool_dependencies_check_box_checked = False
+        else:
+            install_tool_dependencies_check_box_checked = True
+        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
         return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako',
                                     repository=repository,
-                                    readme_text=readme_text,
                                     no_changes_check_box=no_changes_check_box,
                                     original_section_name=original_section_name,
+                                    install_repository_dependencies_check_box=install_repository_dependencies_check_box,
                                     install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+                                    containers_dict=containers_dict,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
                                     encoded_repo_info_dict=tool_shed_encode( repo_info_dict ),
                                     repo_info_dict=repo_info_dict,
-                                    includes_tool_dependencies=includes_tool_dependencies,
                                     message=message,
                                     status=status )
     @web.expose
@@ -1714,41 +1751,6 @@
                                                           status=status ) )
     @web.expose
     @web.require_admin
-    def view_readme( self, trans, id, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        cntrller = params.get( 'cntrller', 'admin_toolshed' )
-        status = params.get( 'status', 'done' )
-        repository = get_installed_tool_shed_repository( trans, id )
-        metadata = repository.metadata
-        shed_config_dict = repository.get_shed_config_dict( trans.app )
-        tool_path = shed_config_dict.get( 'tool_path', None )
-        if metadata and 'readme' in metadata:
-            readme_filename = metadata[ 'readme' ]
-            if tool_path:
-                readme_filename = os.path.join( tool_path, readme_filename )
-            try:
-                f = open( readme_filename, 'r' )
-                raw_text = f.read()
-                f.close()
-                readme_text = raw_text
-            except Exception, e:
-                log.debug( "Error attempting to read README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \
-                           ( str( readme_filename ), str( repository.name ), str( repository.changeset_revision ), str( e ) ) )
-                readme_text = ''
-        else:
-            readme_text = ''
-        is_malicious = False
-        return trans.fill_template( '/webapps/community/common/view_readme.mako',
-                                    cntrller=cntrller,
-                                    repository=repository,
-                                    changeset_revision=repository.changeset_revision,
-                                    readme_text=readme_text,
-                                    is_malicious=is_malicious,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_admin
     def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/browse_repository.mako
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -18,9 +18,6 @@
     <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
-        %if repository.has_readme:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>
         %if repository.can_reset_metadata:
             <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='reset_repository_metadata', id=trans.security.encode_id( repository.id ) )}">Reset repository metadata</a>


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/browse_tool_dependency.mako
--- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako
+++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
@@ -20,9 +20,6 @@
     <li><a class="action-button" id="tool_dependency-${tool_dependency.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="tool_dependency-${tool_dependency.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
-        %if repository.has_readme:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>
         %if repository.can_reset_metadata:


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/common.mako
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -1,3 +1,5 @@
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
 <%def name="browse_files(title_text, directory_path)"><script type="text/javascript">
         $(function(){
@@ -67,146 +69,107 @@
     </script></%def>
 
-<%def name="render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )">
-    <% import os %>
+<%def name="render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )">
+    <style type="text/css">
+        #dependency_table{ table-layout:fixed;
+                           width:100%;
+                           overflow-wrap:normal;
+                           overflow:hidden;
+                           border:0px; 
+                           word-break:keep-all;
+                           word-wrap:break-word;
+                           line-break:strict; }
+    </style>
+    <%
+        class RowCounter( object ):
+            def __init__( self ):
+                self.count = 0
+            def increment( self ):
+                self.count += 1
+            def __str__( self ):
+                return str( self.count )
+
+        repository_dependencies_root_folder = containers_dict[ 'repository_dependencies' ]
+        tool_dependencies_root_folder = containers_dict[ 'tool_dependencies' ]
+        env_settings_heaader_row_displayed = False
+        package_header_row_displayed = False
+    %><div class="form-row"><div class="toolParamHelp" style="clear: both;"><p>
-                These tool dependencies can be automatically handled with the installed repository, providing significant benefits, and 
+                These dependencies can be automatically handled with the installed repository, providing significant benefits, and 
                 Galaxy includes various features to manage them.
             </p></div></div>
-    <div class="form-row">
-        <label>Handle tool dependencies?</label>
-        <% disabled = trans.app.config.tool_dependency_dir is None %>
-        ${install_tool_dependencies_check_box.get_html( disabled=disabled )}
-        <div class="toolParamHelp" style="clear: both;">
-            %if disabled:
-                Set the tool_dependency_dir configuration value in your universe_wsgi.ini to automatically handle tool dependencies.
-            %else:
-                Un-check to skip automatic handling of these tool dependencies.
+    %if repository_dependencies_root_folder:
+        <div class="form-row">
+            <label>Handle repository dependencies?</label>
+            ${install_repository_dependencies_check_box.get_html()}
+            <div class="toolParamHelp" style="clear: both;">
+                Un-check to skip automatic installation of these additional repositories required by this repository.
+            </div>
+        </div>
+        <div style="clear: both"></div>
+        <div class="form-row">
+            %if repository_dependencies_root_folder:
+                <p/>
+                <% row_counter = RowCounter() %>
+                <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table">
+                    ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                </table>
             %endif
+            <div style="clear: both"></div></div>
-    </div>
-    <div style="clear: both"></div>
-    <div class="form-row">
-        <style type="text/css">
-            #dependency_table{ table-layout:fixed;
-                               width:100%;
-                               overflow-wrap:normal;
-                               overflow:hidden;
-                               border:0px; 
-                               word-break:keep-all;
-                               word-wrap:break-word;
-                               line-break:strict; }
-        </style>
-        <table class="grid" id="dependency_table">
-            <tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr>
-            <%
-                env_settings_heaader_row_displayed = False
-                package_header_row_displayed = False
-            %>
-            %for repo_info_dict in repo_info_dicts:
-                %for repository_name, repo_info_tuple in repo_info_dict.items():
-                    <% description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple %>
-                    %if tool_dependencies:
-                        <%
-                            # See if tool dependencies are packages, environment settings or both.
-                            contains_packages = False
-                            for k in tool_dependencies.keys():
-                                if k != 'set_environment':
-                                    contains_packages = True
-                                    break
-                            contains_env_settings = 'set_environment' in tool_dependencies.keys()
-                        %>
-                        %if contains_packages:
-                            %if not package_header_row_displayed:
-                                <%
-                                    info_str = "Each of these packages may require their own build requirements (e.g., CMake, g++, etc).  "
-                                    info_str += "Galaxy will not attempt to install these build requirements, so tool dependency installation "
-                                    info_str += "may partially fail if any are missing from your environment, but the repository and all of it's "
-                                    info_str += "contents will be installed.  You can install the missing build requirements and have Galaxy attempt "
-                                    info_str += "to install the packages again if tool dependency installation fails in any way."
-                                %>
-                                </tr><td bgcolor="#FFFFCC" colspan="4">${info_str}</td></tr>
-                                <tr>
-                                    <th>Name</th>
-                                    <th>Version</th>
-                                    <th>Type</th>
-                                    <th>Install directory</th>
-                                </tr>
-                                <% package_header_row_displayed = True %>
-                            %endif
-                            %for dependency_key, requirements_dict in tool_dependencies.items():
-                                %if dependency_key not in [ 'set_environment' ]:
-                                    <%
-                                        name = requirements_dict[ 'name' ]
-                                        version = requirements_dict[ 'version' ]
-                                        type = requirements_dict[ 'type' ]
-                                        install_dir = os.path.join( trans.app.config.tool_dependency_dir,
-                                                                    name,
-                                                                    version,
-                                                                    repository_owner,
-                                                                    repository_name,
-                                                                    changeset_revision )
-                                        tool_dependency_readme_text = requirements_dict.get( 'readme', None )
-                                    %>
-                                    %if not os.path.exists( install_dir ):
-                                        <tr>
-                                            <td>${name}</td>
-                                            <td>${version}</td>
-                                            <td>${type}</td>
-                                            <td>${install_dir}</td>
-                                        </tr>
-                                        %if tool_dependency_readme_text:
-                                            <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
-                                            <tr><td colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr>
-                                        %endif
-                                    %endif
-                                %endif
-                            %endfor
-                        %endif
-                        %if contains_env_settings:
-                            <% environment_settings = tool_dependencies[ 'set_environment' ] %>
-                            %if not env_settings_heaader_row_displayed:
-                                <%
-                                    info_str = "Each of these environment settings will be defined in a file named env.sh in the installation directory."
-                                %>
-                                </tr><td bgcolor="#FFFFCC" colspan="4">${info_str}</td></tr>
-                                <tr>
-                                    <th>Name</th>
-                                    <th>Type</th>
-                                    <th colspan="2">Install directory for environment shell file</th>
-                                </tr>
-                                <% env_settings_heaader_row_displayed = True %>
-                            %endif
-                            %for environment_setting_dict in environment_settings:
-                                <%
-                                    name = environment_setting_dict[ 'name' ]
-                                    type = environment_setting_dict[ 'type' ]
-                                    install_dir = os.path.join( trans.app.config.tool_dependency_dir,
-                                                                'environment_settings',
-                                                                name,
-                                                                repository_owner,
-                                                                repository_name,
-                                                                changeset_revision )
-                                %>
-                                %if not os.path.exists( install_dir ):
-                                    <tr>
-                                        <td>${name}</td>
-                                        <td>${type}</td>
-                                        <td colspan="2">${install_dir}</td>
-                                    </tr>
-                                %endif
-                            %endfor
-                        %endif
-                    %endif
-                %endfor
-            %endfor
-        </table>
+    %endif
+    %if tool_dependencies_root_folder:
+        <div class="form-row">
+            <label>Handle tool dependencies?</label>
+            <% disabled = trans.app.config.tool_dependency_dir is None %>
+            ${install_tool_dependencies_check_box.get_html( disabled=disabled )}
+            <div class="toolParamHelp" style="clear: both;">
+                %if disabled:
+                    Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
+                %else:
+                    Un-check to skip automatic handling of these tool dependencies.
+                %endif
+            </div>
+        </div><div style="clear: both"></div>
-    </div>
+        <div class="form-row">
+            %if tool_dependencies_root_folder:
+                <p/>
+                <% row_counter = RowCounter() %>
+                <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="dependency_table">
+                    ${render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                </table>
+            %endif
+            <div style="clear: both"></div>
+        </div>
+    %endif
+</%def>
+
+<%def name="render_readme_section( containers_dict )">
+    <%
+        class RowCounter( object ):
+            def __init__( self ):
+                self.count = 0
+            def increment( self ):
+                self.count += 1
+            def __str__( self ):
+                return str( self.count )
+
+        readme_files_root_folder = containers_dict[ 'readme_files' ]
+    %>
+    %if readme_files_root_folder:
+        <p/>
+        <div class="form-row">
+            <% row_counter = RowCounter() %>
+            <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table">
+                ${render_folder( readme_files_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+            </table>
+        </div>
+    %endif
 </%def><%def name="dependency_status_updater()">


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
--- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
+++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
@@ -7,9 +7,6 @@
     <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
-        %if repository.has_readme:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>
         %if repository.can_reset_metadata:


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/manage_repository.mako
--- a/templates/admin/tool_shed_repository/manage_repository.mako
+++ b/templates/admin/tool_shed_repository/manage_repository.mako
@@ -14,9 +14,6 @@
         %elif repository.can_install:
             <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ), operation='install' )}">Install</a>
         %elif repository.can_uninstall:
-            %if repository.has_readme:
-                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-            %endif
             <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>
             %if repository.can_reset_metadata:


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
@@ -1,19 +1,33 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_tool_dependency_section" />
-<%namespace file="/webapps/community/common/common.mako" import="render_readme" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
 
 %if message:
     ${render_msg( message, status )}
 %endif
 
 <div class="toolForm">
-    <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div><div class="toolFormBody"><form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ), repo_info_dict=encoded_repo_info_dict )}" method="post" ><div style="clear: both"></div>
-            %if includes_tool_dependencies:
-                ${render_tool_dependency_section( install_tool_dependencies_check_box, [ repo_info_dict ] )}
+            <% readme_files_dict = containers_dict[ 'readme_files' ] %>
+            %if readme_files_dict:
+                <div class="form-row">
+                    <table class="colored" width="100%">
+                        <th bgcolor="#EBD9B2">Repository README file (may contain important installation or license information)</th>
+                    </table>
+                </div>
+                ${render_readme_section( containers_dict )}
+                <div style="clear: both"></div>
+            %endif
+            %if includes_repository_dependencies or includes_tool_dependencies:
+                <div class="form-row">
+                    <table class="colored" width="100%">
+                        <th bgcolor="#EBD9B2">Confirm dependency installation</th>
+                    </table>
+                </div>
+                ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )}
             %endif
             <div style="clear: both"></div><div class="form-row">
@@ -43,6 +57,3 @@
         </form></div></div>
-%if readme_text:
-    ${render_readme( readme_text )}
-%endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -1,7 +1,19 @@
 <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_tool_dependency_section" />
-<%namespace file="/webapps/community/common/common.mako" import="render_readme" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )}
+    ${container_javascripts()}
+</%def>
 
 %if message:
     ${render_msg( message, status )}
@@ -21,26 +33,34 @@
         general questions or concerns.
     </p></div>
-<br/>
-
 <div class="toolForm">
-    %if includes_tool_dependencies and trans.app.config.use_tool_dependencies:
-        <div class="toolFormTitle">Confirm tool dependency installation</div>
-    %else:
-        <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div>
-    %endif
     <div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div>
-            %if includes_tool_dependencies and trans.app.config.use_tool_dependencies:
-                ${render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )}
-                <div style="clear: both"></div>
+            <% readme_files_dict = containers_dict[ 'readme_files' ] %>
+            %if readme_files_dict:
                 <div class="form-row"><table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
+                        <th bgcolor="#EBD9B2">Repository README file (may contain important installation or license information)</th></table></div>
+                ${render_readme_section( containers_dict )}
+                <div style="clear: both"></div>
             %endif
+            %if includes_repository_dependencies or ( includes_tool_dependencies and trans.app.config.use_tool_dependencies ):
+                <div class="form-row">
+                    <table class="colored" width="100%">
+                        <th bgcolor="#EBD9B2">Confirm dependency installation</th>
+                    </table>
+                </div>
+                ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )}
+                <div style="clear: both"></div>
+            %endif
+            <div class="form-row">
+                <table class="colored" width="100%">
+                    <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
+                </table>
+            </div>
             %if shed_tool_conf_select_field:
                 <div class="form-row"><label>Shed tool configuration file:</label>
@@ -77,6 +97,3 @@
         </form></div></div>
-%if readme_text:
-    ${render_readme( readme_text )}
-%endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
@@ -7,9 +7,6 @@
 <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
-        %if repository.has_readme:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/admin/tool_shed_repository/view_tool_metadata.mako
--- a/templates/admin/tool_shed_repository/view_tool_metadata.mako
+++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako
@@ -5,9 +5,6 @@
 <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
-        %if repository_metadata and 'readme' in repository_metadata:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_readme', id=trans.security.encode_id( repository.id ) )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/common/common.mako
--- a/templates/webapps/community/common/common.mako
+++ b/templates/webapps/community/common/common.mako
@@ -57,29 +57,6 @@
     ${html}
 </%def>
 
-<%def name="render_readme( readme_text )">
-    <style type="text/css">
-        #readme_table{ table-layout:fixed;
-                       width:100%;
-                       overflow-wrap:normal;
-                       overflow:hidden;
-                       border:0px; 
-                       word-break:keep-all;
-                       word-wrap:break-word;
-                       line-break:strict; }
-    </style>
-    <div class="toolForm">
-        <div class="toolFormTitle">Repository README file (may contain important installation or license information)</div>
-        <div class="toolFormBody">
-            <div class="form-row">
-                <table id="readme_table">
-                    <tr><td>${ escape_html_add_breaks( readme_text ) }</td></tr>
-                </table>
-            </div>
-        </div>
-    </div>
-</%def>
-
 <%def name="render_long_description( description_text )"><style type="text/css">
         #description_table{ table-layout:fixed;


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/common/view_readme.mako
--- a/templates/webapps/community/common/view_readme.mako
+++ /dev/null
@@ -1,88 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/webapps/community/common/common.mako" import="render_readme" />
-
-<%
-    if trans.webapp.name == 'community':
-        is_admin = trans.user_is_admin()
-        is_new = repository.is_new( trans.app )
-        can_contact_owner = trans.user and trans.user != repository.user
-        can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
-        can_rate = not is_new and trans.user and repository.user != trans.user
-        can_upload = can_push
-        can_download = not is_new and ( not is_malicious or can_push )
-        can_browse_contents = not is_new
-        can_view_change_log = not is_new
-        can_manage = is_admin or repository.user == trans.user
-        if can_push:
-            browse_label = 'Browse or delete repository tip files'
-        else:
-            browse_label = 'Browse repository tip files'
-%>
-
-<br/><br/>
-<ul class="manage-table-actions">
-    %if trans.webapp.name == 'community':
-        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
-        <div popupmenu="repository-${repository.id}-popup">
-            %if can_manage:
-                <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a>
-            %else:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
-            %endif
-            %if can_upload:
-                <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
-            %endif
-            %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
-            %endif
-            %if can_rate:
-                <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
-            %endif
-            %if can_browse_contents:
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label | h}</a>
-            %endif
-            %if can_contact_owner:
-                <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a>
-            %endif
-            %if can_download:
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
-            %endif
-        </div>
-    %else:
-        %if cntrller=='repository':
-            <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ) )}">Preview tools for install</a></li>       
-            <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
-            <div popupmenu="repository-${repository.id}-popup">
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a>
-            </div>
-        %else:
-            <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
-            <div popupmenu="repository-${repository.id}-popup">
-                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
-                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a>
-                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a>
-                %if repository.includes_tools:
-                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a>
-                %endif
-                %if repository.tool_dependencies:
-                    <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %>
-                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a>
-                %endif
-                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
-            </div>
-        %endif
-    %endif
-</ul>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-%if readme_text:
-    ${render_readme( readme_text )}
-%endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/browse_repository.mako
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -77,9 +77,6 @@
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
             %endif
-            %if has_readme:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a>
-            %endif
             %if can_view_change_log:
                 <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
             %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -1,3 +1,5 @@
+<%namespace file="/webapps/community/common/common.mako" import="escape_html_add_breaks" />
+
 <%def name="common_javascripts(repository)"><script type="text/javascript">
         $(function(){
@@ -75,7 +77,7 @@
     </script></%def>
 
-<%def name="dependency_javascripts()">
+<%def name="container_javascripts()"><script type="text/javascript">
         var init_dependencies = function() {
             var storage_id = "library-expand-state-${trans.security.encode_id(10000)}";
@@ -199,30 +201,29 @@
             ><%
                 col_span_str = ''
+                folder_label = str( folder.label )
                 if folder.datatypes:
-                    label = folder.label
                     col_span_str = 'colspan="4"'
                 elif folder.label == 'Repository dependencies':
-                    label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder.label
-                elif folder.repository_dependencies:
-                    label = folder.label
+                    folder_label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder_label
+                elif folder.key == 'readme_files':
+                    folder_label = "%s<i> - may contain important installation or license information</i>" % folder_label
                 elif folder.invalid_tools:
-                    label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder.label
+                    folder_label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder_label
                 elif folder.tool_dependencies:
-                    label = "%s<i> - this repository's tools require installation of these dependencies</i>" % folder.label
+                    folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label
                     col_span_str = 'colspan="3"'
                 elif folder.valid_tools:
-                    label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder.label
+                    folder_label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder_label
                     col_span_str = 'colspan="3"'
                 elif folder.workflows:
-                    label = folder.label
                     col_span_str = 'colspan="4"'
             %><td ${col_span_str} style="padding-left: ${folder_pad}px;"><span class="expandLink folder-${encoded_id}-click"><div style="float: left; margin-left: 2px;" class="expandLink folder-${encoded_id}-click"><a class="folder-${encoded_id}-click" href="javascript:void(0);">
-                            ${label}
+                            ${folder_label}
                         </a></div></span>
@@ -236,6 +237,9 @@
     %for sub_folder in folder.folders:
         ${render_folder( sub_folder, pad, parent=my_row, row_counter=row_counter, is_root_folder=False )}
     %endfor
+    %for readme in folder.readme_files:
+        ${render_readme( readme, pad, my_row, row_counter )}
+    %endfor
     %for repository_dependency in folder.repository_dependencies:
         ${render_repository_dependency( repository_dependency, pad, my_row, row_counter )}
     %endfor
@@ -298,9 +302,30 @@
         %endif
         id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
-            <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision )}">
+            %if invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision:
+                <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision )}">
+                    ${invalid_tool.tool_config | h}
+                </a>
+            %else:
                 ${invalid_tool.tool_config | h}
-            </a>
+            %endif
+        </td>
+    </tr>
+    <%
+        my_row = row_counter.count
+        row_counter.increment()
+    %>
+</%def>
+
+<%def name="render_readme( readme, pad, parent, row_counter )">
+    <% encoded_id = trans.security.encode_id( readme.id ) %>
+    <tr class="datasetRow"
+        %if parent is not None:
+            parent="${parent}"
+        %endif
+        id="libraryItem-${encoded_id}">
+        <td style="padding-left: ${pad+20}px;">
+            ${escape_html_add_breaks( readme.text )}
         </td></tr><%
@@ -311,14 +336,19 @@
 
 <%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter )">
                 
-    <% encoded_id = trans.security.encode_id( repository_dependency.id ) %>
+    <%
+        encoded_id = trans.security.encode_id( repository_dependency.id )
+        repository_name = str( repository_dependency.repository_name )
+        changeset_revision = str( repository_dependency.changeset_revision )
+        repository_owner = str( repository_dependency.repository_owner )
+    %><tr class="datasetRow"
         %if parent is not None:
             parent="${parent}"
         %endif
         id="libraryItem-${encoded_id}">
         ##<td style="padding-left: ${pad+20}px;">${repository_dependency.toolshed | h}</td>
-        <td style="padding-left: ${pad+20}px;">Repository <b>${repository_dependency.repository_name | h}</b> revision <b>${repository_dependency.changeset_revision | h}</b> owned by <b>${repository_dependency.repository_owner | h}</b></td>
+        <td style="padding-left: ${pad+20}px;">Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b></td></tr><%
         my_row = row_counter.count
@@ -385,6 +415,9 @@
             ${version_str | h}
         </${cell_type}><${cell_type}>${tool_dependency.type | h}</${cell_type}>
+        %if tool_dependency.install_dir:
+            <${cell_type}>${tool_dependency.install_dir | h}</${cell_type}>
+        %endif
     </tr><%
         my_row = row_counter.count
@@ -428,17 +461,18 @@
         from galaxy.tool_shed.encoding_util import tool_shed_encode
 
         has_datatypes = metadata and 'datatypes' in metadata
-        has_readme = metadata and 'readme' in metadata
+        has_readme_files = metadata and 'readme_files' in metadata
         has_workflows = metadata and 'workflows' in metadata
         
         datatypes_root_folder = containers_dict[ 'datatypes' ]
         invalid_tools_root_folder = containers_dict[ 'invalid_tools' ]
+        readme_files_root_folder = containers_dict[ 'readme_files' ]
         repository_dependencies_root_folder = containers_dict[ 'repository_dependencies' ]
         tool_dependencies_root_folder = containers_dict[ 'tool_dependencies' ]
         valid_tools_root_folder = containers_dict[ 'valid_tools' ]
         workflows_root_folder = containers_dict[ 'workflows' ]
         
-        has_contents = datatypes_root_folder, invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder
+        has_contents = datatypes_root_folder or invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder
 
         class RowCounter( object ):
             def __init__( self ):
@@ -448,6 +482,18 @@
             def __str__( self ):
                 return str( self.count )
     %>
+    %if readme_files_root_folder:
+        <div class="toolForm">
+            <div class="toolFormTitle">Repository README files (may contain important installation or license information)</div>
+            <div class="toolFormBody">
+                <p/>
+                <% row_counter = RowCounter() %>
+                <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="readme_files">
+                    ${render_folder( readme_files_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                </table>
+            </div>
+        </div>
+    %endif
     %if repository_dependencies_root_folder or tool_dependencies_root_folder:
         <div class="toolForm"><div class="toolFormTitle">Dependencies of this repository</div>
@@ -455,15 +501,15 @@
                 %if repository_dependencies_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="repository_dependencies">
-                        ${self.render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="repository_dependencies">
+                        ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
                 %if tool_dependencies_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="tool_dependencies">
-                        ${self.render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="tool_dependencies">
+                        ${render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
             </div>
@@ -477,29 +523,29 @@
                 %if valid_tools_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="valid_tools">
-                        ${self.render_folder( valid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_tools">
+                        ${render_folder( valid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
                 %if invalid_tools_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="invalid_tools">
-                        ${self.render_folder( invalid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_tools">
+                        ${render_folder( invalid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
                 %if workflows_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="workflows">
-                        ${self.render_folder( workflows_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="workflows">
+                        ${render_folder( workflows_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
                 %if datatypes_root_folder:
                     <p/><% row_counter = RowCounter() %>
-                    <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="datatypes">
-                        ${self.render_folder( datatypes_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="datatypes">
+                        ${render_folder( datatypes_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
                     </table>
                 %endif
             </div>


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/contact_owner.mako
--- a/templates/webapps/community/repository/contact_owner.mako
+++ b/templates/webapps/community/repository/contact_owner.mako
@@ -43,9 +43,6 @@
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
             %endif
-            %if has_readme:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a>
-            %endif
             %if can_view_change_log:
                 <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
             %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/manage_repository.mako
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -5,23 +5,26 @@
 
 <%
     from galaxy.web.framework.helpers import time_ago
+
+    has_metadata = repository.metadata_revisions
+    has_readme = metadata and 'readme' in metadata
     is_admin = trans.user_is_admin()
     is_new = repository.is_new( trans.app )
     is_deprecated = repository.deprecated
+
+    can_browse_contents = not is_new
     can_contact_owner = trans.user and trans.user != repository.user
+    can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated
     can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository )
+    can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
+    can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user
+    can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0
+    can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
+    can_set_metadata = not is_new and not is_deprecated
+    can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app )
+    can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated
     can_upload = can_push
-    can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
-    can_browse_contents = not is_new
-    can_set_metadata = not is_new and not is_deprecated
-    can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user
     can_view_change_log = not is_new
-    can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app )
-    can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated
-    can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated
-    can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0
-    has_readme = metadata and 'readme' in metadata
-    can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
     reviewing_repository = cntrller and cntrller == 'repository_review'
 
     if can_push:
@@ -51,7 +54,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )}
-    ${dependency_javascripts()}
+    ${container_javascripts()}
 </%def><br/><br/>
@@ -78,9 +81,6 @@
                 %if can_upload:
                     <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
                 %endif
-                %if has_readme:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-                %endif
                 %if can_view_change_log:
                     <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
                 %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/preview_tools_in_changeset.mako
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -36,7 +36,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )}
-    ${dependency_javascripts()}
+    ${container_javascripts()}
 </%def><br/><br/>
@@ -44,9 +44,6 @@
     <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup">
-        %if has_readme:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a>


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/rate_repository.mako
--- a/templates/webapps/community/repository/rate_repository.mako
+++ b/templates/webapps/community/repository/rate_repository.mako
@@ -84,9 +84,6 @@
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
             %endif
-            %if has_readme:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a>
-            %endif
             %if can_view_change_log:
                 <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
             %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/tool_form.mako
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -147,9 +147,6 @@
                         %if can_upload:
                             <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
                         %endif
-                        %if has_readme:
-                            <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-                        %endif
                         %if can_view_change_log:
                             <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
                         %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/view_changelog.mako
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -52,9 +52,6 @@
         %else:
             <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
         %endif
-        %if has_readme:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a>
-        %endif
         %if can_rate:
             <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.security.encode_id( repository.id ) )}">Rate repository</a>
         %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/view_changeset.mako
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -53,9 +53,6 @@
         %else:
             <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
         %endif
-        %if has_readme:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a>
-        %endif
         %if can_view_change_log:
             <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
         %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/view_repository.mako
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -5,22 +5,26 @@
 
 <%
     from galaxy.web.framework.helpers import time_ago
+
+    has_readme = metadata and 'readme' in metadata
+    has_metadata = repository.metadata_revisions
     is_new = repository.is_new( trans.app )
     is_deprecated = repository.deprecated
+
+    can_browse_contents = trans.webapp.name == 'community' and not is_new
     can_contact_owner = trans.user and trans.user != repository.user
+    can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
     can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_rate = not is_deprecated and not is_new and trans.user and repository.user != trans.user
+    can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
     can_upload = can_push
-    can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
-    can_browse_contents = trans.webapp.name == 'community' and not is_new
     can_view_change_log = trans.webapp.name == 'community' and not is_new
+    reviewing_repository = cntrller and cntrller == 'repository_review'
+
     if can_push:
         browse_label = 'Browse or delete repository tip files'
     else:
         browse_label = 'Browse repository tip files'
-    has_readme = metadata and 'readme' in metadata
-    reviewing_repository = cntrller and cntrller == 'repository_review'
-    can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
 %><%!
@@ -40,7 +44,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )}
-    ${dependency_javascripts()}
+    ${container_javascripts()}
 </%def><br/><br/>
@@ -68,9 +72,6 @@
                     %if can_upload:
                         <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
                     %endif
-                    %if has_readme:
-                        <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-                    %endif
                     %if can_view_change_log:
                         <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
                     %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/view_tool_metadata.mako
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -6,23 +6,27 @@
 <%
     from galaxy.web.framework.helpers import time_ago
     from urllib import quote_plus
+
+    has_metadata = repository.metadata_revisions
+    has_readme = metadata and 'readme' in metadata
     is_admin = trans.user_is_admin()
     is_new = repository.is_new( trans.app )
     is_deprecated = repository.deprecated
+
+    can_browse_contents = trans.webapp.name == 'community' and not is_new
     can_contact_owner = trans.user and trans.user != repository.user
+    can_download = not is_new and ( not is_malicious or can_push )
+    can_manage = is_admin or repository.user == trans.user
     can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
+    can_rate = repository.user != trans.user
+    can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
     can_upload = can_push
-    can_download = not is_new and ( not is_malicious or can_push )
-    can_browse_contents = trans.webapp.name == 'community' and not is_new
-    can_rate = repository.user != trans.user
-    can_manage = is_admin or repository.user == trans.user
     can_view_change_log = trans.webapp.name == 'community' and not is_new
+
     if can_push:
         browse_label = 'Browse or delete repository tip files'
     else:
         browse_label = 'Browse repository tip files'
-    has_readme = metadata and 'readme' in metadata
-    can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
 %><%!
@@ -69,9 +73,6 @@
                 %if can_upload:
                     <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
                 %endif
-                %if has_readme:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-                %endif
                 %if can_view_change_log:
                     <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
                 %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 templates/webapps/community/repository/view_workflow.mako
--- a/templates/webapps/community/repository/view_workflow.mako
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -55,9 +55,6 @@
                 %else:
                     <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
                 %endif
-                %if has_readme:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a>
-                %endif
                 %if can_view_change_log:
                     <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
                 %endif


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -134,12 +134,6 @@
         tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) )
         tc.submit( 'select_files_to_delete_button' )
         self.check_for_strings( strings_displayed, strings_not_displayed )
-    def display_readme_file( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ):
-        if changeset_revision is None:
-            changeset_revision = self.get_repository_tip( repository )
-        repository_id = self.security.encode_id( repository.id )
-        self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) )
-        self.check_for_strings( strings_displayed, strings_not_displayed )
     def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ):
         url = '/repos/%s/%s' % ( owner_name, repository_name )
         self.visit_url( url )


diff -r 88aba66bb81351cbd625ca7fb9ed39874016b36a -r 14589278b02d0dea916319811ddebf17ecca0747 test/tool_shed/functional/test_0000_basic_repository_features.py
--- a/test/tool_shed/functional/test_0000_basic_repository_features.py
+++ b/test/tool_shed/functional/test_0000_basic_repository_features.py
@@ -105,7 +105,7 @@
                           commit_message="Uploaded filtering.txt", 
                           uncompress_file='No', 
                           remove_repo_files_not_in_tar='No' )
-        self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
+        self.manage_repository( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
     def test_0055_upload_filtering_test_data( self ):
         '''Upload filtering test data.'''
         repository = get_repository_by_name_and_owner( repository_name, admin_username )
@@ -137,22 +137,16 @@
         '''Upload readme.txt file associated with tool version 2.2.0.'''
         repository = get_repository_by_name_and_owner( repository_name, admin_username )
         self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" )
-        self.display_readme_file( repository, strings_displayed=[ 'This is a readme file.' ] )
+        self.manage_repository( repository, strings_displayed=[ 'This is a readme file.' ] )
         # Verify that there is a different readme file for each metadata revision.
         metadata_revisions = self.get_repository_metadata_revisions( repository )
-        strings_to_check = [ 'Readme file for filtering 1.1.0', 'This is a readme file.' ]
-        for key, metadata_revision in enumerate( metadata_revisions ):
-            # Metadata revisions are in order newest to oldest at this point.
-            self.display_readme_file( repository, metadata_revision, strings_not_displayed=[ strings_to_check[ key ] ] )
+        self.manage_repository( repository, strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] )
     def test_0075_delete_readme_txt_file( self ):
         '''Delete the readme.txt file.'''
         repository = get_repository_by_name_and_owner( repository_name, admin_username )
         self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] )
         self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 )
-        # Deleting a readme file for a specific revision should make the repository fall back 
-        # to a previous revision's readme file, if one exists.
-        # TODO: All readme files should be displayed.
-        self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
+        self.manage_repository( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
     def test_0080_search_for_valid_filter_tool( self ):
         '''Verify that the "search for valid tool" feature finds the filtering tool.'''
         repository = get_repository_by_name_and_owner( repository_name, admin_username )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

--

This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.

    

Bitbucket

tags

participants (1)