commit/galaxy-central: greg: Refinements for installing and managing tool dependencies for tools contained in installed tool shed repositories.

22 Jun 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/db2bf8004964/
changeset:   db2bf8004964
user:        greg
date:        2012-06-22 16:21:09
summary:     Refinements for installing and managing tool dependencies for tools contained in installed tool shed repositories.
affected #:  26 files

diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2647,6 +2647,12 @@
     pass
 
 class ToolShedRepository( object ):
+    installation_status = Bunch( CLONED='cloned',
+                                 SETTING_TOOL_VERSIONS='setting tool versions',
+                                 INSTALLING_TOOL_DEPENDENCIES='installing tool dependencies',
+                                 INSTALLED='installed',
+                                 ERROR='error',
+                                 UNINSTALLED='uninstalled' )
     def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None,
                   changeset_revision=None, ctx_rev=None, metadata=None, includes_datatypes=False, update_available=False, deleted=False,
                   uninstalled=False, dist_to_shed=False ):
@@ -2696,47 +2702,59 @@
         """Return the repository's tool dependencies that are currently installed."""
         installed_dependencies = []
         for tool_dependency in self.tool_dependencies:
-            if not tool_dependency.uninstalled:
+            if tool_dependency.status == ToolDependency.installation_status.INSTALLED:
                 installed_dependencies.append( tool_dependency )
         return installed_dependencies
     @property
     def missing_tool_dependencies( self ):
         """Return the repository's tool dependencies that are not currently installed, and may not ever have been installed."""
         missing_dependencies = []
-        # Get the dependency information from the metadata for comparison against the installed tool dependencies.
-        tool_dependencies = self.metadata.get( 'tool_dependencies', None )
-        if tool_dependencies:
-            for dependency_key, requirements_dict in tool_dependencies.items():
-                name = requirements_dict[ 'name' ]
-                version = requirements_dict[ 'version' ]
-                type = requirements_dict[ 'type' ]
-                if self.tool_dependencies:
-                    found = False
-                    for tool_dependency in self.tool_dependencies:
-                        if tool_dependency.name==name and tool_dependency.version==version and tool_dependency.type==type:
-                            found = True
-                            if tool_dependency.uninstalled:
-                                missing_dependencies.append( ( tool_dependency.name, tool_dependency.version, tool_dependency.type ) )
-                                break
-                    if not found:
-                        missing_dependencies.append( ( name, version, type ) )
+        for tool_dependency in self.tool_dependencies:
+            if tool_dependency.status in [ ToolDependency.installation_status.NEVER_INSTALLED,
+                                           ToolDependency.installation_status.ERROR,
+                                           ToolDependency.installation_status.UNINSTALLED ]:
+                missing_dependencies.append( tool_dependency )
         return missing_dependencies
     @property
+    def tool_dependencies_being_installed( self ):
+        dependencies_being_installed = []
+        for tool_dependency in self.tool_dependencies:
+            if tool_dependency.status == ToolDependency.installation_status.INSTALLING:
+                dependencies_being_installed.append( tool_dependency )
+        return dependencies_being_installed
+    @property
+    def tool_dependencies_with_installation_errors( self ):
+        dependencies_with_installation_errors = []
+        for tool_dependency in self.tool_dependencies:
+            if tool_dependency.status == ToolDependency.installation_status.ERROR:
+                dependencies_with_installation_errors.append( tool_dependency )
+        return dependencies_with_installation_errors
+    @property
     def uninstalled_tool_dependencies( self ):
         """Return the repository's tool dependencies that have been uninstalled."""
         uninstalled_tool_dependencies = []
         for tool_dependency in self.tool_dependencies:
-            if tool_dependency.uninstalled:
+            if tool_dependency.status == ToolDependency.installation_status.UNINSTALLED:
                 uninstalled_tool_dependencies.append( tool_dependency )
         return uninstalled_tool_dependencies
 
 class ToolDependency( object ):
-    def __init__( self, tool_shed_repository_id=None, name=None, version=None, type=None, uninstalled=False ):
+    installation_status = Bunch( NEVER_INSTALLED='Never installed',
+                                 INSTALLING='Installing',
+                                 INSTALLED='Installed',
+                                 ERROR='Error',
+                                 UNINSTALLED='Uninstalled' )
+    states = Bunch( INSTALLING = 'running',
+                    OK = 'ok',
+                    ERROR = 'error',
+                    UNINSTALLED = 'deleted_new' )
+    def __init__( self, tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None ):
         self.tool_shed_repository_id = tool_shed_repository_id
         self.name = name
         self.version = version
         self.type = type
-        self.uninstalled = uninstalled
+        self.status = status
+        self.error_message = error_message
     def installation_directory( self, app ):
         return os.path.join( app.config.tool_dependency_dir,
                              self.name,


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -398,7 +398,8 @@
     Column( "name", TrimmedString( 255 ) ),
     Column( "version", Text ),
     Column( "type", TrimmedString( 40 ) ),
-    Column( "uninstalled", Boolean, default=False ) )
+    Column( "status", TrimmedString( 255 ), nullable=False ),
+    Column( "error_message", TEXT ) )
 
 ToolVersion.table = Table( "tool_version", metadata,
     Column( "id", Integer, primary_key=True ),


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
@@ -0,0 +1,63 @@
+"""
+Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    col = Column( "status", TrimmedString( 255 ), nullable=False )
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.status
+    except Exception, e:
+        print "Adding status column to the tool_dependency table failed: %s" % str( e )
+    col = Column( "error_message", TEXT )
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.error_message
+    except Exception, e:
+        print "Adding error_message column to the tool_dependency table failed: %s" % str( e )
+    try:
+        ToolDependency_table.c.uninstalled.drop()
+    except Exception, e:
+        print "Dropping uninstalled column from the tool_dependency table failed: %s" % str( e )
+def downgrade():
+    metadata.reflect()
+    ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+    try:
+        ToolDependency_table.c.status.drop()
+    except Exception, e:
+        print "Dropping column status from the tool_dependency table failed: %s" % str( e )
+    try:
+        ToolDependency_table.c.error_message.drop()
+    except Exception, e:
+        print "Dropping column error_message from the tool_dependency table failed: %s" % str( e )
+    col = Column( "uninstalled", Boolean, default=False )
+    try:
+        col.create( ToolDependency_table )
+        assert col is ToolDependency_table.c.uninstalled
+    except Exception, e:
+        print "Adding uninstalled column to the tool_dependency table failed: %s" % str( e )


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/tool_shed/install_manager.py
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -7,7 +7,6 @@
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
 from galaxy.util.odict import odict
-from galaxy.tool_shed.migrate.common import *
 
 REPOSITORY_OWNER = 'devteam'
 
@@ -177,7 +176,7 @@
                     status, message = handle_tool_dependencies( app=self.app,
                                                                 tool_shed_repository=tool_shed_repository,
                                                                 tool_dependencies_config=tool_dependencies_config )
-                    if status != 'ok' and message:
+                    if status != 'done' and message:
                         print 'The following error occurred from the InstallManager while installing tool dependencies:'
                         print message
                 add_to_tool_panel( self.app,


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/tool_shed/tool_dependencies/common_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py
@@ -1,10 +1,6 @@
 import os, shutil, tarfile, urllib2
 from galaxy.datatypes.checkers import *
 
-MISCELLANEOUS_ACTIONS = [ 'change_directory' ]
-MOVE_ACTIONS = [ 'move_directory_files', 'move_file' ]
-ALL_ACTIONS = MISCELLANEOUS_ACTIONS + MOVE_ACTIONS
-
 def extract_tar( file_name, file_path ):
     if isgzip( file_name ) or isbz2( file_name ):
         # Open for reading with transparent compression.


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
@@ -13,6 +13,8 @@
 
 from fabric.api import env, lcd, local, settings
 
+INSTALLATION_LOG = 'INSTALLATION.log'
+
 def check_fabric_version():
     version = env.version
     if int( version.split( "." )[ 0 ] ) < 1:
@@ -32,16 +34,19 @@
     yield work_dir
     if os.path.exists( work_dir ):
         local( 'rm -rf %s' % work_dir )
-def handle_post_build_processing( tool_dependency_dir, install_dir, env_dependency_path, package_name=None ):
+def handle_post_build_processing( app, tool_dependency, install_dir, env_dependency_path, package_name=None ):
+    sa_session = app.model.context.current
     cmd = "echo 'PATH=%s:$PATH; export PATH' > %s/env.sh;chmod +x %s/env.sh" % ( env_dependency_path, install_dir, install_dir )
-    message = ''
     output = local( cmd, capture=True )
-    log_results( cmd, output, os.path.join( install_dir, 'env_sh.log' ) )
+    log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) )
     if output.return_code:
-        message = '%s  %s' % ( message, str( output.stderr ) )
-    return message
-def install_and_build_package( params_dict ):
+        tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+        tool_dependency.error_message = str( output.stderr )
+        sa_session.add( tool_dependency )
+        sa_session.flush()
+def install_and_build_package( app, tool_dependency, params_dict ):
     """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
+    sa_session = app.model.context.current
     install_dir = params_dict[ 'install_dir' ]
     download_url = params_dict.get( 'download_url', None )
     clone_cmd = params_dict.get( 'clone_cmd', None )
@@ -59,43 +64,38 @@
                     dir = work_dir
             elif clone_cmd:
                 output = local( clone_cmd, capture=True )
-                log_results( clone_cmd, output, os.path.join( install_dir, 'clone_repository.log' ) )
+                log_results( clone_cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) )
                 if output.return_code:
-                    return '%s.  ' % str( output.stderr )
+                    tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+                    tool_dependency.error_message = str( output.stderr )
+                    sa_session.add( tool_dependency )
+                    sa_session.flush()
+                    return
                 dir = package_name
             if actions:
                 with lcd( dir ):
                     current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
                     for action_tup in actions:
                         action_key, action_dict = action_tup
-                        if action_key.find( 'v^v^v' ) >= 0:
-                            action_items = action_key.split( 'v^v^v' )
-                            action_name = action_items[ 0 ]
-                            action = action_items[ 1 ]
-                        elif action_key in common_util.ALL_ACTIONS:
-                            action_name = action_key
-                        else:
-                            action_name = None
-                        if action_name:
-                            if action_name == 'change_directory':
-                                current_dir = os.path.join( current_dir, action )
-                                lcd( current_dir )
-                            elif action_name == 'move_directory_files':
-                                common_util.move_directory_files( current_dir=current_dir,
-                                                                  source_dir=os.path.join( action_dict[ 'source_directory' ] ),
-                                                                  destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )
-                            elif action_name == 'move_file':
-                                common_util.move_file( current_dir=current_dir,
-                                                       source=os.path.join( action_dict[ 'source' ] ),
-                                                       destination_dir=os.path.join( action_dict[ 'destination' ] ) )
+                        if action_key == 'move_directory_files':
+                            common_util.move_directory_files( current_dir=current_dir,
+                                                              source_dir=os.path.join( action_dict[ 'source_directory' ] ),
+                                                              destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )
+                        elif action_key == 'move_file':
+                            common_util.move_file( current_dir=current_dir,
+                                                   source=os.path.join( action_dict[ 'source' ] ),
+                                                   destination_dir=os.path.join( action_dict[ 'destination' ] ) )
                         else:
                             action = action_key
                             with settings( warn_only=True ):
                                 output = local( action, capture=True )
-                                log_results( action, output, os.path.join( install_dir, 'actions.log' ) )
+                                log_results( action, output, os.path.join( install_dir, INSTALLATION_LOG ) )
                                 if output.return_code:
-                                    return '%s.  ' % str( output.stderr )
-    return ''
+                                    tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+                                    tool_dependency.error_message = str( output.stderr )
+                                    sa_session.add( tool_dependency )
+                                    sa_session.flush()
+                                    return
 def log_results( command, fabric_AttributeString, file_path ):
     """
     Write attributes of fabric.operations._AttributeString (which is the output of executing command using fabric's local() method)
@@ -105,12 +105,12 @@
         logfile = open( file_path, 'ab' )
     else:
         logfile = open( file_path, 'wb' )
-    logfile.write( "\n#############################################" )
-    logfile.write( '\n%s\nSTDOUT\n' % command )
+    logfile.write( "\n#############################################\n" )
+    logfile.write( '%s\nSTDOUT\n' % command )
     logfile.write( str( fabric_AttributeString.stdout ) )
-    logfile.write( "#############################################\n" )
-    logfile.write( "\n#############################################" )
-    logfile.write( '\n%s\nSTDERR\n' % command )
+    logfile.write( "\n#############################################\n" )
+    logfile.write( "\n#############################################\n" )
+    logfile.write( '%s\nSTDERR\n' % command )
     logfile.write( str( fabric_AttributeString.stderr ) )
-    logfile.write( "#############################################\n" )
+    logfile.write( "\n#############################################\n" )
     logfile.close()


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -11,19 +11,16 @@
 from elementtree import ElementTree, ElementInclude
 from elementtree.ElementTree import Element, SubElement
 
-def create_or_update_tool_dependency( app, tool_shed_repository, name, version, type ):
+def create_or_update_tool_dependency( app, tool_shed_repository, name, version, type, status ):
     # Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled repository is being reinstalled.
+    sa_session = app.model.context.current
     # First see if an appropriate tool_dependency record exists for the received tool_shed_repository.
-    sa_session = app.model.context.current
     tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, name, version, type )
     if tool_dependency:
-        tool_dependency.uninstalled = False
+        tool_dependency.status = status
     else:
         # Create a new tool_dependency record for the tool_shed_repository.
-        tool_dependency = app.model.ToolDependency( tool_shed_repository_id=tool_shed_repository.id,
-                                                    name=name,
-                                                    version=version,
-                                                    type=type )
+        tool_dependency = app.model.ToolDependency( tool_shed_repository.id, name, version, type, status )
     sa_session.add( tool_dependency )
     sa_session.flush()
     return tool_dependency
@@ -42,14 +39,15 @@
                                           repository.owner,
                                           repository.name,
                                           repository.installed_changeset_revision ) )
-def install_package( app, elem, tool_shed_repository, name=None, version=None ):
-    # If name and version are not None, then a specific tool dependency is being installed.
-    message = ''
+def install_package( app, elem, tool_shed_repository, tool_dependencies=None ):
+    # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository.
+    sa_session = app.model.context.current
+    tool_dependency = None
     # The value of package_name should match the value of the "package" type in the tool config's <requirements> tag set, but it's not required.
     package_name = elem.get( 'name', None )
     package_version = elem.get( 'version', None )
     if package_name and package_version:
-        if ( not name and not version ) or ( name and version and name==package_name and version==package_version ):
+        if tool_dependencies:
             install_dir = get_tool_dependency_install_dir( app, tool_shed_repository, package_name, package_version )
             if not os.path.exists( install_dir ):
                 for package_elem in elem:
@@ -66,26 +64,22 @@
                         # Handle tool dependency installation using a fabric method included in the Galaxy framework.
                         fabfile_path = None
                     for method_elem in package_elem:
-                        error_message = run_fabric_method( app,
-                                                           method_elem,
-                                                           fabfile_path,
-                                                           app.config.tool_dependency_dir,
-                                                           install_dir,
-                                                           package_name=package_name )
-                        if error_message:
-                            message += '%s' % error_message
-                        else:
-                            tool_dependency = create_or_update_tool_dependency( app,
-                                                                                tool_shed_repository,
-                                                                                name=package_name,
-                                                                                version=package_version,
-                                                                                type='package' )
+                        tool_dependency = create_or_update_tool_dependency( app,
+                                                                            tool_shed_repository,
+                                                                            name=package_name,
+                                                                            version=package_version,
+                                                                            type='package',
+                                                                            status=app.model.ToolDependency.installation_status.INSTALLING )
+                        run_fabric_method( app, tool_dependency, method_elem, fabfile_path, install_dir, package_name=package_name )
+                        sa_session.refresh( tool_dependency )
+                        if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
                             print package_name, 'version', package_version, 'installed in', install_dir
             else:
                 print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n'
-    return message
-def run_fabric_method( app, elem, fabfile_path, tool_dependency_dir, install_dir, package_name=None, **kwd ):
+    return tool_dependency
+def run_fabric_method( app, tool_dependency, elem, fabfile_path, install_dir, package_name=None, **kwd ):
     """Parse a tool_dependency.xml file's fabfile <method> tag set to build the method parameters and execute the method."""
+    sa_session = app.model.context.current
     if not os.path.exists( install_dir ):
         os.makedirs( install_dir )
     # Default value for env_dependency_path.
@@ -109,7 +103,7 @@
                         action_key = action_elem.text.replace( '$INSTALL_DIR', install_dir )
                         if not action_key:
                             continue
-                    elif action_type in MOVE_ACTIONS:
+                    elif action_type in [ 'move_directory_files', 'move_file' ]:
                         # Examples:
                         # <action type="move_file">
                         #     <source>misc/some_file</source>
@@ -124,9 +118,6 @@
                             move_elem_text = move_elem.text.replace( '$INSTALL_DIR', install_dir )
                             if move_elem_text:
                                 action_dict[ move_elem.tag ] = move_elem_text
-                    elif action_elem.text:
-                        # Example: <action type="change_directory">bin</action>
-                        action_key = '%sv^v^v%s' % ( action_type, action_elem.text )
                     else:
                         continue
                     actions.append( ( action_key, action_dict ) )
@@ -141,24 +132,36 @@
         params_dict[ 'package_name' ] = package_name
     if fabfile_path:
         # TODO: Handle this using the fabric api.
-        # run_proprietary_fabric_method( app, elem, fabfile_path, tool_dependency_dir, install_dir, package_name=package_name )
+        # run_proprietary_fabric_method( app, elem, fabfile_path, install_dir, package_name=package_name )
         return 'Tool dependency installation using proprietary fabric scripts is not yet supported.  '
     else:
         # There is currently only 1 fabric method, install_and_build_package().
         try:
-            message = install_and_build_package( params_dict )
-            if message:
-                return message
+            install_and_build_package( app, tool_dependency, params_dict )
         except Exception, e:
-            return '%s.  ' % str( e )
-        try:
-            message = handle_post_build_processing( tool_dependency_dir, install_dir, env_dependency_path, package_name=package_name )
-            if message:
-                return message
-        except:
-            return '%s.  ' % str( e )
-        return ''
-def run_proprietary_fabric_method( app, elem, fabfile_path, tool_dependency_dir, install_dir, package_name=None, **kwd ):
+            tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+            tool_dependency.error_message = str( e )
+            sa_session.add( tool_dependency )
+            sa_session.flush()
+        sa_session.refresh( tool_dependency )
+        if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
+            try:
+                handle_post_build_processing( app,
+                                              tool_dependency,
+                                              install_dir,
+                                              env_dependency_path,
+                                              package_name=package_name )
+            except Exception, e:
+                tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+                tool_dependency.error_message = str( e )
+                sa_session.add( tool_dependency )
+                sa_session.flush()
+        sa_session.refresh( tool_dependency )
+        if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
+            tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
+            sa_session.add( tool_dependency )
+            sa_session.flush()
+def run_proprietary_fabric_method( app, elem, fabfile_path, install_dir, package_name=None, **kwd ):
     """
     TODO: Handle this using the fabric api.
     Parse a tool_dependency.xml file's fabfile <method> tag set to build the method parameters and execute the method.
@@ -193,7 +196,7 @@
         return "Exception executing fabric script %s: %s.  " % ( str( fabfile_path ), str( e ) )
     if returncode:
         return message    
-    message = handle_post_build_processing( tool_dependency_dir, install_dir, env_dependency_path, package_name=package_name )
+    message = handle_post_build_processing( app, tool_dependency, install_dir, env_dependency_path, package_name=package_name )
     if message:
         return message
     else:


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -6,7 +6,7 @@
 from galaxy.datatypes.checkers import *
 from galaxy.util.json import *
 from galaxy.tools.search import ToolBoxSearch
-from galaxy.tool_shed.tool_dependencies.install_util import install_package
+from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package
 from galaxy.tool_shed.encoding_util import *
 from galaxy.model.orm import *
 
@@ -318,8 +318,8 @@
     # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed.
     if current_changeset_revision is None:
         # The current_changeset_revision is not passed if a repository is being installed for the first time.  If a previously installed repository
-        # was later uninstalled, this value should be received as the value of that change set to which the repository had been updated just prior to
-        # it being uninstalled.
+        # was later uninstalled, this value should be received as the value of that change set to which the repository had been updated just prior
+        # to it being uninstalled.
         current_changeset_revision = installed_changeset_revision
     sa_session = app.model.context.current  
     tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
@@ -353,6 +353,37 @@
     sa_session.add( tool_shed_repository )
     sa_session.flush()
     return tool_shed_repository
+def create_tool_dependency_objects( app, tool_shed_repository, current_changeset_revision ):
+    # Create or update a ToolDependency for each entry in tool_dependencies_config.  This method is called when installing a new tool_shed_repository.
+    tool_dependency_objects = []
+    work_dir = make_tmp_directory()
+    # Get the tool_dependencies.xml file from the repository.
+    tool_dependencies_config = get_config_from_repository( app,
+                                                           'tool_dependencies.xml',
+                                                           tool_shed_repository,
+                                                           current_changeset_revision,
+                                                           work_dir )
+    tree = ElementTree.parse( tool_dependencies_config )
+    root = tree.getroot()
+    ElementInclude.include( root )
+    fabric_version_checked = False
+    for elem in root:
+        if elem.tag == 'package':
+            package_name = elem.get( 'name', None )
+            package_version = elem.get( 'version', None )
+            if package_name and package_version:
+                tool_dependency = create_or_update_tool_dependency( app,
+                                                                    tool_shed_repository,
+                                                                    name=package_name,
+                                                                    version=package_version,
+                                                                    type='package',
+                                                                    status=app.model.ToolDependency.installation_status.NEVER_INSTALLED )
+                tool_dependency_objects.append( tool_dependency )
+    try:
+        shutil.rmtree( work_dir )
+    except:
+        pass
+    return tool_dependency_objects
 def generate_clone_url( trans, repository ):
     """Generate the URL for cloning a repository."""
     tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
@@ -1163,7 +1194,7 @@
         message = str( e )
         error = True
     return error, message
-def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, name=None, version=None, type='package' ):
+def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies=None ):
     """
     Install and build tool dependencies defined in the tool_dependencies_config.  This config's tag sets can currently refer to installation
     methods in Galaxy's tool_dependencies module.  In the future, proprietary fabric scripts contained in the repository will be supported.
@@ -1171,7 +1202,7 @@
     will be installed in:
     ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision>
     """
-    status = 'ok'
+    status = 'done'
     message = ''
     # Parse the tool_dependencies.xml config.
     tree = ElementTree.parse( tool_dependencies_config )
@@ -1179,12 +1210,24 @@
     ElementInclude.include( root )
     fabric_version_checked = False
     for elem in root:
-        if elem.tag == type:
-            error_message = install_package( app, elem, tool_shed_repository, name=name, version=version )
-            if error_message:
-                message += '  %s' % error_message
-    if message:
-        status = 'error'
+        if elem.tag == 'package':
+            package_name = elem.get( 'name', None )
+            package_version = elem.get( 'version', None )
+            if package_name and package_version:
+                can_install = True
+                if tool_dependencies:
+                    # Only install the package if it is not already installed.
+                    can_install = False
+                    for tool_dependency in tool_dependencies:
+                        if tool_dependency.name==package_name and tool_dependency.version==package_version:
+                            can_install = tool_dependency.status in [ app.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                                      app.model.ToolDependency.installation_status.UNINSTALLED ]
+                            break
+                if can_install:
+                    tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
+                    if tool_dependency and tool_dependency.status == app.model.ToolDependency.installation_status.ERROR:
+                        message = tool_dependency.error_message
+                        status = 'error'
     return status, message
 def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ):
     """
@@ -1247,13 +1290,11 @@
     # Load or deactivate proprietary datatype display applications
     app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate )
 def load_repository_contents( trans, repository_name, description, owner, installed_changeset_revision, current_changeset_revision, ctx_rev,
-                              tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, shed_tool_conf=None,
-                              install_tool_dependencies=False ):
+                              tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, shed_tool_conf=None ):
     """
     Generate the metadata for the installed tool shed repository, among other things.  This method is called from Galaxy (never the tool shed)
     when an admin is installing a new repository or reinstalling an uninstalled repository.
     """
-    message = ''
     metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url )
     # Add a new record to the tool_shed_repository table if one doesn't already exist.  If one exists but is marked deleted, undelete it.  This
     # must happen before the call to add_to_tool_panel() below because tools will not be properly loaded if the repository is marked deleted.
@@ -1285,20 +1326,6 @@
             repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups )
             # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance.
             copy_sample_files( trans.app, sample_files, sample_files_copied=sample_files_copied )
-            if install_tool_dependencies and 'tool_dependencies' in metadata_dict:
-                # Get the tool_dependencies.xml file from the repository.
-                tool_dependencies_config = get_config_from_repository( trans.app,
-                                                                       'tool_dependencies.xml',
-                                                                       tool_shed_repository,
-                                                                       current_changeset_revision,
-                                                                       work_dir )
-                # Install dependencies for repository tools.
-                status, message = handle_tool_dependencies( app=trans.app,
-                                                            tool_shed_repository=tool_shed_repository,
-                                                            tool_dependencies_config=tool_dependencies_config )
-                if status != 'ok' and message:
-                    print 'The following error occurred from load_repository_contents while installing tool dependencies:'
-                    print message
             add_to_tool_panel( app=trans.app,
                                repository_name=repository_name,
                                repository_clone_url=repository_clone_url,
@@ -1340,7 +1367,9 @@
             shutil.rmtree( work_dir )
         except:
             pass
-    return tool_shed_repository, metadata_dict, message
+    if 'tool_dependencies' in metadata_dict:
+        tool_dependencies = create_tool_dependency_objects( trans.app, tool_shed_repository, current_changeset_revision )
+    return tool_shed_repository, metadata_dict
 def make_tmp_directory():
     tmp_dir = os.getenv( 'TMPDIR', '' )
     if tmp_dir:
@@ -1505,7 +1534,7 @@
         error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) )
         log.debug( error_message )
     if removed:
-        tool_dependency.uninstalled = True
+        tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED
         trans.sa_session.add( tool_dependency )
         trans.sa_session.flush()
     return removed, error_message


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -77,9 +77,71 @@
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( self.model_class )
 
+class ToolDependencyGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_dependency ):
+            return tool_dependency.name
+    class VersionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_dependency ):
+            return tool_dependency.version
+    class TypeColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_dependency ):
+            return tool_dependency.type
+    class StatusColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_dependency ):
+            if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLING ]:
+                return tool_dependency.status
+            else:
+                if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                               trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                    bgcolor = trans.model.ToolDependency.states.UNINSTALLED
+                elif tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR ]:
+                    bgcolor = trans.model.ToolDependency.states.ERROR
+                elif tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED ]:
+                    bgcolor = trans.model.ToolDependency.states.OK
+                rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">' % ( bgcolor, trans.security.encode_id( tool_dependency.id ) )
+                rval += '%s</div>' % tool_dependency.status
+                return rval
+
+    webapp = "galaxy"
+    title = "Tool Dependencies"
+    template = "admin/tool_shed_repository/tool_dependencies_grid.mako"
+    model_class = model.ToolDependency
+    default_sort_key = "-create_time"
+    num_rows_per_page = 50
+    preserve_state = True
+    use_paging = False
+    columns = [
+        NameColumn( "Name",
+                    filterable="advanced" ),
+        VersionColumn( "Version",
+                       filterable="advanced" ),
+        TypeColumn( "Type",
+                    filterable="advanced" ),
+        StatusColumn( "Installation Status",
+                      filterable="advanced" ),
+    ]
+    operations = [
+        grids.GridOperation( "Install",
+                             allow_multiple=True,
+                             condition=( lambda item: item.status in [ model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                                       model.ToolDependency.installation_status.UNINSTALLED ] ) ),
+        grids.GridOperation( "Uninstall",
+                             allow_multiple=True,
+                             allow_popup=False,
+                             condition=( lambda item: item.status in [ model.ToolDependency.installation_status.INSTALLED,
+                                                                      model.ToolDependency.installation_status.ERROR ] ) )
+    ]
+    def apply_query_filter( self, trans, query, **kwd ):
+        tool_dependency_id = kwd.get( 'tool_dependency_id', None )
+        if not tool_dependency_id:
+            return query
+        return query.filter_by( tool_dependency_id=trans.security.decode_id( tool_dependency_id ) )
+
 class AdminToolshed( AdminGalaxy ):
     
     repository_list_grid = RepositoryListGrid()
+    tool_dependency_grid = ToolDependencyGrid()
 
     @web.expose
     @web.require_admin
@@ -153,9 +215,8 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] )
-        repository = get_repository( trans, kwd[ 'repository_id' ] )
         return trans.fill_template( '/admin/tool_shed_repository/browse_tool_dependency.mako',
-                                    repository=repository,
+                                    repository=tool_dependency.tool_shed_repository,
                                     tool_dependency=tool_dependency,
                                     message=message,
                                     status=status )
@@ -187,6 +248,35 @@
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
+    def confirm_tool_dependency_install( self, trans, **kwd ):
+        """Display a page enabling the Galaxy administrator to choose to install tool dependencies for a tool shed repository they are installing."""
+        # This method is called from the tool shed (never Galaxy) when a tool shed repository that includes a file named tool_dependencies.xml
+        # is being installed into a local Galaxy instance.
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        repo_info_dict = kwd[ 'repo_info_dict' ]
+        includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
+        # Decode the encoded repo_info_dict param value.
+        dict_with_tool_dependencies = tool_shed_decode( repo_info_dict )
+        # The repo_info_dict includes tool dependencies which we need to display so the user knows what will be installed.
+        new_repo_info_dict = {}
+        for name, repo_info_tuple in dict_with_tool_dependencies.items():
+            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+            # Create a new repo_info_dict by eliminating tool-dependencies from the repo_info_tuple.
+            new_repo_info_dict[ name ] = ( description, repository_clone_url, changeset_revision, ctx_rev )
+        repo_info_dict = tool_shed_encode( new_repo_info_dict )
+        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
+        return trans.fill_template( '/admin/tool_shed_repository/confirm_tool_dependency_install.mako',
+                                    tool_shed_url=tool_shed_url,
+                                    repo_info_dict=repo_info_dict,
+                                    dict_with_tool_dependencies=dict_with_tool_dependencies,
+                                    includes_tools=includes_tools,
+                                    install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
     def deactivate_or_uninstall_repository( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
@@ -270,71 +360,33 @@
         return get_repository_file_contents( file_path )
     @web.expose
     @web.require_admin
-    def install_missing_tool_dependencies( self, trans, **kwd ):
-        """
-        Install dependencies for tools included in the repository that were not installed when the repository was installed or that are
-        being reinstalled after the repository was uninstalled.
-        """
-        reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) )
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
-        repository = get_repository( trans, kwd[ 'id' ] )
-        install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
-        if not reinstalling and install_tool_dependencies and kwd.get( 'install_missing_tool_dependencies_button', False ):
-            shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
-            repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
-            # Get the tool_dependencies.xml file from the repository.
-            work_dir = make_tmp_directory()
-            tool_dependencies_config = get_config_from_repository( trans.app,
-                                                                   'tool_dependencies.xml',
-                                                                   repository,
-                                                                   repository.changeset_revision,
-                                                                   work_dir,
-                                                                   install_dir=relative_install_dir )
-            status, message = handle_tool_dependencies( app=trans.app,
-                                                        tool_shed_repository=repository,
-                                                        tool_dependencies_config=tool_dependencies_config )
-            try:
-                shutil.rmtree( work_dir )
-            except:
-                pass
-            return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
-                                        repository=repository,
-                                        description=repository.description,
-                                        repo_files_dir=repo_files_dir,
-                                        message=message,
-                                        status=status )
-        if reinstalling and kwd.get( 'install_missing_tool_dependencies_button', False ):
-            # The user has been presented the option to install tool dependencies, so redirect to reinstall the repository, sending
-            # along the user's choice.
-            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                              action='reinstall_repository',
-                                                              **kwd ) )
-        tool_dependencies = repository.metadata[ 'tool_dependencies' ]
-        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
-        if not reinstalling:
-            # Filter the tool_dependencies dictionary to eliminate successfully installed dependencies.
-            filtered_tool_dependencies = {}
-            for missing_dependency_tup in repository.missing_tool_dependencies:
-                name, version, type = missing_dependency_tup
-                dependency_key = '%s/%s' % ( name, version )
-                install_dir = get_tool_dependency_install_dir( trans.app, repository, name, version )
-                filtered_tool_dependencies[ dependency_key ] = dict( name=name, type=type, version=version )
-            tool_dependencies = filtered_tool_dependencies
-        no_changes = kwd.get( 'no_changes', '' )
-        no_changes_checked = CheckboxField.is_checked( no_changes )
-        new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
-        tool_panel_section = kwd.get( 'tool_panel_section', '' )
-        return trans.fill_template( '/admin/tool_shed_repository/install_missing_tool_dependencies.mako',
-                                    repository=repository,
-                                    reinstalling=reinstalling,
-                                    tool_dependencies=tool_dependencies,
-                                    no_changes_checked=no_changes_checked,
-                                    new_tool_panel_section=new_tool_panel_section,
-                                    tool_panel_section=tool_panel_section,
-                                    install_tool_dependencies_check_box=install_tool_dependencies_check_box,
-                                    message=message,
-                                    status=status )
+    def initiate_tool_dependency_installation( self, trans, tool_dependencies ):
+        """Install specified dependencies for repository tools."""
+        # Get the tool_shed_repository from one of the tool_dependencies.
+        tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
+        work_dir = make_tmp_directory()
+        # Get the tool_dependencies.xml file from the repository.
+        tool_dependencies_config = get_config_from_repository( trans.app,
+                                                               'tool_dependencies.xml',
+                                                               tool_shed_repository,
+                                                               tool_shed_repository.changeset_revision,
+                                                               work_dir )
+        status, message = handle_tool_dependencies( app=trans.app,
+                                                    tool_shed_repository=tool_shed_repository,
+                                                    tool_dependencies_config=tool_dependencies_config,
+                                                    tool_dependencies=tool_dependencies )
+        try:
+            shutil.rmtree( work_dir )
+        except:
+            pass
+        tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ]
+        if not message:
+            message = "Installed tool dependencies: %s" % ','.join( td.name for td in tool_dependencies )
+        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                          action='manage_tool_dependencies',
+                                                          tool_dependency_ids=tool_dependency_ids,
+                                                          message=message,
+                                                          status=status ) )
     @web.expose
     @web.require_admin
     def install_repository( self, trans, **kwd ):
@@ -413,23 +465,19 @@
                     clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev )
                     owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
                     tool_shed = clean_tool_shed_url( tool_shed_url )
-                    tool_shed_repository, metadata_dict, error_message = load_repository_contents( trans,
-                                                                                                   repository_name=name,
-                                                                                                   description=description,
-                                                                                                   owner=owner,
-                                                                                                   installed_changeset_revision=changeset_revision,
-                                                                                                   current_changeset_revision=changeset_revision,
-                                                                                                   ctx_rev=ctx_rev,
-                                                                                                   tool_path=tool_path,
-                                                                                                   repository_clone_url=repository_clone_url,
-                                                                                                   relative_install_dir=relative_install_dir,
-                                                                                                   tool_shed=tool_shed,
-                                                                                                   tool_section=tool_section,
-                                                                                                   shed_tool_conf=shed_tool_conf,
-                                                                                                   install_tool_dependencies=install_tool_dependencies )
-                    if error_message:
-                        message += error_message
-                        status = 'error'
+                    tool_shed_repository, metadata_dict, = load_repository_contents( trans,
+                                                                                     repository_name=name,
+                                                                                     description=description,
+                                                                                     owner=owner,
+                                                                                     installed_changeset_revision=changeset_revision,
+                                                                                     current_changeset_revision=changeset_revision,
+                                                                                     ctx_rev=ctx_rev,
+                                                                                     tool_path=tool_path,
+                                                                                     repository_clone_url=repository_clone_url,
+                                                                                     relative_install_dir=relative_install_dir,
+                                                                                     tool_shed=tool_shed,
+                                                                                     tool_section=tool_section,
+                                                                                     shed_tool_conf=shed_tool_conf )
                     if 'tools' in metadata_dict:
                         # Get the tool_versions from the tool shed for each tool in the installed change set.
                         url = '%srepository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \
@@ -449,26 +497,28 @@
             if installed_repository_names:                
                 installed_repository_names.sort()
                 num_repositories_installed = len( installed_repository_names )
-                if install_tool_dependencies:
-                    dependency_str = ' along with tool dependencies '
-                else:
-                    dependency_str = ''
                 if tool_section:
-                    message += 'Installed %d %s%sand all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
+                    message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
                         ( num_repositories_installed,
                           inflector.cond_plural( num_repositories_installed, 'repository' ),
-                          dependency_str,
                           tool_section.name )
                 else:
-                    message += 'Installed %d %s%s and all tools were loaded into the tool panel outside of any sections.<br/>Installed repositories: ' % \
+                    message += 'Installed %d %s and all tools were loaded into the tool panel outside of any sections.<br/>Installed repositories: ' % \
                         ( num_repositories_installed,
-                          inflector.cond_plural( num_repositories_installed, 'repository' ),
-                          dependency_str )
+                          inflector.cond_plural( num_repositories_installed, 'repository' ) )
                 for i, repo_name in enumerate( installed_repository_names ):
                     if i == len( installed_repository_names ) -1:
                         message += '%s.<br/>' % repo_name
                     else:
                         message += '%s, ' % repo_name
+            if install_tool_dependencies:
+                tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.missing_tool_dependencies ]
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='manage_tool_dependencies',
+                                                                  operation='install',
+                                                                  tool_dependency_ids=tool_dependency_ids,
+                                                                  status=status,
+                                                                  message=message ) )
             return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
                                                               action='browse_repositories',
                                                               message=message,
@@ -520,61 +570,42 @@
     @web.expose
     @web.require_admin
     def install_tool_dependencies( self, trans, **kwd ):
-        """Install dependencies for tools included in the repository when the repository is being installed."""
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        repo_info_dict = kwd[ 'repo_info_dict' ]
-        includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
-        # Decode the encoded repo_info_dict param value.
-        dict_with_tool_dependencies = tool_shed_decode( repo_info_dict )
-        # The repo_info_dict includes tool dependencies which we need to display so the user knows what will be installed.
-        new_repo_info_dict = {}
-        for name, repo_info_tuple in dict_with_tool_dependencies.items():
-            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
-            # Create a new repo_info_dict by eliminating tool-dependencies from the repo_info_tuple.
-            new_repo_info_dict[ name ] = ( description, repository_clone_url, changeset_revision, ctx_rev )
-        repo_info_dict = tool_shed_encode( new_repo_info_dict )
-        install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        tool_dependency_ids = util.listify( params.get( 'tool_dependency_ids', None ) )
+        if not tool_dependency_ids:
+            tool_dependency_ids = util.listify( params.get( 'id', None ) )
+        tool_dependencies = []
+        for tool_dependency_id in tool_dependency_ids:
+            tool_dependency = get_tool_dependency( trans, tool_dependency_id )
+            tool_dependencies.append( tool_dependency )
+        if kwd.get( 'install_tool_dependencies_button', False ):
+            # Filter tool dependencies to only those that are installed.
+            tool_dependencies_for_installation = []
+            for tool_dependency in tool_dependencies:
+                if tool_dependency.status in [ trans.model.ToolDependency.installation_status.UNINSTALLED,
+                                               trans.model.ToolDependency.installation_status.ERROR ]:
+                    tool_dependencies_for_installation.append( tool_dependency )
+            if tool_dependencies_for_installation:
+                # Redirect back to the ToolDependencyGrid before initiating installation.
+                tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies_for_installation ]
+                new_kwd = dict( action='manage_tool_dependencies',
+                                operation='initiate_tool_dependency_installation',
+                                tool_dependency_ids=tool_dependency_ids,
+                                message=message,
+                                status=status )
+                return self.tool_dependency_grid( trans, **new_kwd )
+            else:
+                message = 'All of the selected tool dependencies are already installed.'
+                status = 'error'
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='manage_tool_dependencies',
+                                                                  tool_dependency_ids=tool_dependency_ids,
+                                                                  status=status,
+                                                                  message=message ) )
         return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies.mako',
-                                    tool_shed_url=tool_shed_url,
-                                    repo_info_dict=repo_info_dict,
-                                    dict_with_tool_dependencies=dict_with_tool_dependencies,
-                                    includes_tools=includes_tools,
-                                    install_tool_dependencies_check_box=install_tool_dependencies_check_box,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_admin
-    def install_tool_dependency( self, trans, name, version, type, repository_id, **kwd ):
-        """Install dependencies for tools included in the repository when the repository is being installed."""
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
-        repository = get_repository( trans, repository_id )
-        shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
-        repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
-        # Get the tool_dependencies.xml file from the repository.
-        work_dir = make_tmp_directory()
-        tool_dependencies_config = get_config_from_repository( trans.app,
-                                                               'tool_dependencies.xml',
-                                                               repository,
-                                                               repository.changeset_revision,
-                                                               work_dir,
-                                                               install_dir=relative_install_dir )
-        status, message = handle_tool_dependencies( app=trans.app,
-                                                    tool_shed_repository=repository,
-                                                    tool_dependencies_config=tool_dependencies_config,
-                                                    name=name,
-                                                    version=version,
-                                                    type=type )
-        try:
-            shutil.rmtree( work_dir )
-        except:
-            pass
-        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
-                                    repository=repository,
-                                    description=repository.description,
-                                    repo_files_dir=repo_files_dir,
+                                    tool_dependencies=tool_dependencies,
                                     message=message,
                                     status=status )
     @web.expose
@@ -614,12 +645,79 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository_id = kwd[ 'id' ]
-        repository = get_repository( trans, repository_id )
-        return trans.fill_template( '/admin/tool_shed_repository/manage_tool_dependencies.mako',
-                                    repository=repository,
-                                    message=message,
-                                    status=status )
+        tool_dependency_id = params.get( 'tool_dependency_id', None )
+        tool_dependency_ids = util.listify( params.get( 'tool_dependency_ids', None ) )
+        if not tool_dependency_ids:
+            tool_dependency_ids = util.listify( params.get( 'id', None ) )
+        if tool_dependency_id and tool_dependency_id not in tool_dependency_ids:
+            tool_dependency_ids.append( tool_dependency_id )
+        tool_dependencies = []
+        # We need a tool_shed_repository, so get it from one of the tool_dependencies.
+        tool_dependency = get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
+        tool_shed_repository = tool_dependency.tool_shed_repository
+        self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies"  % tool_shed_repository.name
+        self.tool_dependency_grid.global_actions = \
+            [ grids.GridAction( label='Browse repository', 
+                                url_args=dict( controller='admin_toolshed', 
+                                               action='browse_repository', 
+                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
+              grids.GridAction( label='Manage repository', 
+                                url_args=dict( controller='admin_toolshed', 
+                                               action='manage_repository', 
+                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
+              grids.GridAction( label='Get updates', 
+                                url_args=dict( controller='admin_toolshed', 
+                                               action='check_for_updates', 
+                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
+              grids.GridAction( label='Set tool versions', 
+                                url_args=dict( controller='admin_toolshed', 
+                                               action='set_tool_versions', 
+                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
+              grids.GridAction( label='Deactivate or uninstall repository', 
+                                url_args=dict( controller='admin_toolshed', 
+                                               action='deactivate_or_uninstall_repository', 
+                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ) ]
+        if 'operation' in kwd:
+            operation = kwd[ 'operation' ].lower()
+            if not tool_dependency_ids:
+                message = 'Select at least 1 tool dependency to %s.' % operation
+                kwd[ 'message' ] = message
+                kwd[ 'status' ] = 'error'
+                del kwd[ 'operation' ]
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='manage_tool_dependencies',
+                                                                  **kwd ) )
+            if operation == 'browse':
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='browse_tool_dependency',
+                                                                  **kwd ) )
+            elif operation == 'uninstall':
+                tool_dependencies_for_uninstallation = []
+                for tool_dependency_id in tool_dependency_ids:
+                    tool_dependency = get_tool_dependency( trans, tool_dependency_id )
+                    if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED,
+                                                   trans.model.ToolDependency.installation_status.ERROR ]:
+                        tool_dependencies_for_uninstallation.append( tool_dependency )
+                if tool_dependencies_for_uninstallation:
+                    return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                      action='uninstall_tool_dependencies',
+                                                                      **kwd ) )
+                else:
+                    kwd[ 'message' ] = 'All selected tool dependencies are already uninstalled.'
+                    kwd[ 'status' ] = 'error'
+            elif operation == "install":
+                tool_dependencies_for_installation = []
+                for tool_dependency_id in tool_dependency_ids:
+                    tool_dependency = get_tool_dependency( trans, tool_dependency_id )
+                    if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                   trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                        tool_dependencies_for_installation.append( tool_dependency )
+                if tool_dependencies_for_installation:
+                    self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+                else:
+                    kwd[ 'message' ] = 'All selected tool dependencies are already installed.'
+                    kwd[ 'status' ] = 'error'
+        return self.tool_dependency_grid( trans, **kwd )
     @web.json
     @web.require_admin
     def open_folder( self, trans, folder_path ):
@@ -710,39 +808,52 @@
                     tool_section = trans.app.toolbox.tool_panel[ section_key ]
                 else:
                     tool_section = None
-        tool_shed_repository, metadata_dict, error_message = load_repository_contents( trans,
-                                                                                       repository_name=repository.name,
-                                                                                       description=repository.description,
-                                                                                       owner=repository.owner,
-                                                                                       installed_changeset_revision=repository.installed_changeset_revision,
-                                                                                       current_changeset_revision=current_changeset_revision,
-                                                                                       ctx_rev=ctx_rev,
-                                                                                       tool_path=tool_path,
-                                                                                       repository_clone_url=repository_clone_url,
-                                                                                       relative_install_dir=relative_install_dir,
-                                                                                       tool_shed=repository.tool_shed,
-                                                                                       tool_section=tool_section,
-                                                                                       shed_tool_conf=shed_tool_conf,
-                                                                                       install_tool_dependencies=install_tool_dependencies )
-        if error_message:
-            # We'll only have an error_message if there was a problem installing tool dependencies.
-            message += error_message
-            status = 'error'
+        tool_shed_repository, metadata_dict, load_repository_contents( trans,
+                                                                       repository_name=repository.name,
+                                                                       description=repository.description,
+                                                                       owner=repository.owner,
+                                                                       installed_changeset_revision=repository.installed_changeset_revision,
+                                                                       current_changeset_revision=current_changeset_revision,
+                                                                       ctx_rev=ctx_rev,
+                                                                       tool_path=tool_path,
+                                                                       repository_clone_url=repository_clone_url,
+                                                                       relative_install_dir=relative_install_dir,
+                                                                       tool_shed=repository.tool_shed,
+                                                                       tool_section=tool_section,
+                                                                       shed_tool_conf=shed_tool_conf )
         repository.uninstalled = False
         repository.deleted = False
         trans.sa_session.add( repository )
         trans.sa_session.flush()
+        message += 'The <b>%s</b> repository has been reinstalled.  ' % repository.name
         if install_tool_dependencies:
-            dependency_str = ' along with tool dependencies'
-            if error_message:
-                dependency_str += ', but with some errors installing the dependencies'
-        else:
-            dependency_str = ' without tool dependencies'
-        message += 'The <b>%s</b> repository has been reinstalled%s.  ' % ( repository.name, dependency_str )
+            message += 'The following tool dependencies are now being installed, please wait...'
+            tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.missing_tool_dependencies ]
+            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                              action='manage_tool_dependencies',
+                                                              operation='install',
+                                                              tool_dependency_ids=tool_dependency_ids,
+                                                              status=status,
+                                                              message=message ) )
         return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
                                                           action='browse_repositories',
                                                           message=message,
                                                           status=status ) )
+    @web.json
+    def repository_installation_status_updates( self, trans, id=None, status=None ):
+        # Avoid caching
+        trans.response.headers[ 'Pragma' ] = 'no-cache'
+        trans.response.headers[ 'Expires' ] = '0'
+        # Create new HTML for any that have changed
+        rval = {}
+        if id is not None and status is not None:
+            repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
+            if repository.status != status:
+                repository.status = status
+                rval[ id ] = { "status": repository.status,
+                               "html_status": unicode( trans.fill_template( "admin/tool_shed_repository/repository_installation_status.mako",
+                                                                            repository=repository ),
+                                                                            'utf-8' ) }
     @web.expose
     @web.require_admin
     def reselect_tool_panel_section( self, trans, **kwd ):
@@ -811,22 +922,62 @@
                                     repo_files_dir=repo_files_dir,
                                     message=message,
                                     status=status )
+    @web.json
+    def tool_dependency_status_updates( self, trans, ids=None, status_list=None ):
+        # Avoid caching
+        trans.response.headers[ 'Pragma' ] = 'no-cache'
+        trans.response.headers[ 'Expires' ] = '0'
+        # Create new HTML for any that have changed
+        rval = {}
+        if ids is not None and status_list is not None:
+            ids = ids.split( "," )
+            status_list = status_list.split( "," )
+            for id, status in zip( ids, status_list ):
+                tool_dependency = trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) )
+                if tool_dependency.status != status:
+                    rval[ id ] = { "status": tool_dependency.status,
+                                   "html_status": unicode( trans.fill_template( "admin/tool_shed_repository/tool_dependency_installation_status.mako",
+                                                                                tool_dependency=tool_dependency ),
+                                                                                'utf-8' ) }
+        return rval
     @web.expose
     @web.require_admin
-    def uninstall_tool_dependency( self, trans, **kwd ):
+    def uninstall_tool_dependencies( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository( trans, kwd[ 'repository_id' ] )
-        tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] )
-        uninstalled, error_message = remove_tool_dependency( trans, tool_dependency )
-        if uninstalled:
-            message = "The '%s' tool dependency has been uninstalled." % tool_dependency.name
-        else:
-            message = "Error attempting to uninstall the '%s' tool dependency: %s" % ( tool_dependency.name, error_message )
-            status = 'error'
-        return trans.fill_template( '/admin/tool_shed_repository/manage_tool_dependencies.mako',
-                                    repository=repository,
+        tool_dependency_ids = util.listify( params.get( 'tool_dependency_ids', None ) )
+        if not tool_dependency_ids:
+            tool_dependency_ids = util.listify( params.get( 'id', None ) )
+        tool_dependencies = []
+        for tool_dependency_id in tool_dependency_ids:
+            tool_dependency = get_tool_dependency( trans, tool_dependency_id )
+            tool_dependencies.append( tool_dependency )
+        if kwd.get( 'uninstall_tool_dependencies_button', False ):
+            errors = False
+            # Filter tool dependencies to only those that are installed.
+            tool_dependencies_for_uninstallation = []
+            for tool_dependency in tool_dependencies:
+                if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED,
+                                               trans.model.ToolDependency.installation_status.ERROR ]:
+                    tool_dependencies_for_uninstallation.append( tool_dependency )
+            for tool_dependency in tool_dependencies_for_uninstallation:
+                uninstalled, error_message = remove_tool_dependency( trans, tool_dependency )
+                if error_message:
+                    errors = True
+                    message = '%s  %s' % ( message, error_message )
+            if errors:
+                message = "Error attempting to uninstall tool dependencies: %s" % message
+                status = 'error'
+            else:
+                message = "These tool dependencies have been uninstalled: %s" % ','.join( td.name for td in tool_dependencies_for_uninstallation )
+            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                              action='manage_tool_dependencies',
+                                                              tool_dependency_ids=tool_dependency_ids,
+                                                              status=status,
+                                                              message=message ) )
+        return trans.fill_template( '/admin/tool_shed_repository/uninstall_tool_dependencies.mako',
+                                    tool_dependencies=tool_dependencies,
                                     message=message,
                                     status=status )
     @web.expose
@@ -864,11 +1015,14 @@
                     repository.update_available = False
                     trans.sa_session.add( repository )
                     trans.sa_session.flush()
+                    # Create tool_dependency records if necessary.
+                    if 'tool_dependencies' in metadata_dict:
+                        tool_dependencies = create_tool_dependency_objects( trans.app, repository, repository.changeset_revision )
                     message = "The installed repository named '%s' has been updated to change set revision '%s'.  " % ( name, latest_changeset_revision )
                     # See if any tool dependencies can be installed.
                     shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
                     if repository.missing_tool_dependencies:
-                        message += "Select <b>Install tool dependencies</b> from the repository's pop-up menu to install tool dependencies."
+                        message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies."
                 else:
                     message = "The directory containing the installed repository named '%s' cannot be found.  " % name
                     status = 'error'
@@ -951,3 +1105,6 @@
 def get_repository( trans, id ):
     """Get a tool_shed_repository from the database via id"""
     return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
+def get_tool_dependency( trans, id ):
+    """Get a tool_dependency from the database via id"""
+    return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) )


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/web/controllers/tool_runner.py
--- a/lib/galaxy/web/controllers/tool_runner.py
+++ b/lib/galaxy/web/controllers/tool_runner.py
@@ -128,18 +128,17 @@
             else:
                 tool_id_select_field = None
                 tool = tools[ 0 ]
-            if tool.id == job.tool_id and tool.version == job.tool_version:
+            if ( tool.id == job.tool_id or tool.old_id == job.tool_id ) and tool.version == job.tool_version:
                 tool_id_version_message = ''
             elif tool.id == job.tool_id:
                 if job.tool_version == None:
                     # For some reason jobs don't always keep track of the tool version.
                     tool_id_version_message = ''
                 else:
+                    tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available.  ' % job.tool_version
                     if len( tools ) > 1:
-                        tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available.  ' % job.tool_version
                         tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
                     else:
-                        tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available.  ' % job.tool_version
                         tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
             else:
                 if len( tools ) > 1:


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1229,7 +1229,7 @@
         encoded_repo_info_dict = encode( repo_info_dict )
         if includes_tool_dependencies:
             # Redirect back to local Galaxy to present the option to install tool dependencies.
-            url = '%sadmin_toolshed/install_tool_dependencies?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \
+            url = '%sadmin_toolshed/confirm_tool_dependency_install?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \
                 ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) )
         else:
             # Redirect back to local Galaxy to perform install.


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -10,7 +10,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "ui.core", "jquery.dynatree" )}
-    ${common_javascripts(repository.name, repository.repo_files_directory(trans.app))}
+    ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
 </%def><br/><br/>
@@ -21,10 +21,8 @@
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
         %if repository.tool_dependencies:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
-        %endif
-        %if repository.missing_tool_dependencies:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Install missing tool dependencies</a>
+            <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %>
+            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a>
         %endif
     </div></ul>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -10,9 +10,11 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "ui.core", "jquery.dynatree" )}
-    ${common_javascripts(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
+    ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 
+<% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %>
+
 <br/><br/><ul class="manage-table-actions"><li><a class="action-button" id="tool_dependency-${tool_dependency.id}-popup" class="menubutton">Repository Actions</a></li>
@@ -21,8 +23,7 @@
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
-        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
-        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">Uninstall this tool dependency</a>
+        <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></div></ul>
 


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/common.mako
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -1,4 +1,4 @@
-<%def name="common_javascripts(title_text, directory_path)">
+<%def name="browse_files(title_text, directory_path)"><script type="text/javascript">
         $(function(){
             $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) {
@@ -66,3 +66,131 @@
         });
     </script></%def>
+
+<%def name="dependency_status_updater()">
+    <script type="text/javascript">
+
+        // Tool dependency status updater - used to update the installation status on the Tool Dependencies grid. 
+        // Looks for changes in tool dependency installation status using an async request. Keeps calling itself 
+        // (via setTimeout) until dependency installation status is neither 'Installing' nor 'Building'.
+        var tool_dependency_status_updater = function ( dependency_status_list ) {
+            // See if there are any items left to track
+            var empty = true;
+            for ( i in dependency_status_list ) {
+                empty = false;
+                break;
+            }
+            if ( ! empty ) {
+                setTimeout( function() { tool_dependency_status_updater_callback( dependency_status_list ) }, 3000 );
+            }
+        };
+        var tool_dependency_status_updater_callback = function ( dependency_status_list ) {
+            var ids = []
+            var status_list = []
+            $.each( dependency_status_list, function ( id, dependency_status ) {
+                ids.push( id );
+                status_list.push( dependency_status );
+            });
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='admin_toolshed', action='tool_dependency_status_updates' )}",
+                dataType: "json",
+                data: { ids: ids.join( "," ), status_list: status_list.join( "," ) },
+                success : function ( data ) {
+                    $.each( data, function( id, val ) {
+                        // Replace HTML
+                        var cell1 = $("#ToolDependencyStatus-" + id);
+                        cell1.html( val.html_status );
+                        dependency_status_list[ id ] = val.status;
+                    });
+                    tool_dependency_status_updater( dependency_status_list ); 
+                },
+                error: function() {
+                    tool_dependency_status_updater( dependency_status_list ); 
+                }
+            });
+        };
+    </script>
+</%def>
+
+<%def name="tool_dependency_installation_updater()">
+    <% 
+        can_update = False
+        if query.count():
+            # Get the first tool dependency to get to the tool shed repository.
+            tool_dependency = query[0]
+            tool_shed_repository = tool_dependency.tool_shed_repository
+            can_update = tool_shed_repository.tool_dependencies_being_installed or tool_shed_repository.missing_tool_dependencies
+    %>
+    %if can_update:
+        <script type="text/javascript">
+            // Tool dependency installation status updater
+            tool_dependency_status_updater( {${ ",".join( [ '"%s" : "%s"' % ( trans.security.encode_id( td.id ), td.status ) for td in query ] ) }});
+        </script>
+    %endif
+</%def>
+
+<%def name="repository_installation_status_updater()">
+    <script type="text/javascript">
+
+        // Tool shed repository status updater - used to update the installation status on the repository_installation.mako template. 
+        // Looks for changes in repository installation status using an async request. Keeps calling itself (via setTimeout) until
+        // repository installation status is neither 'cloning', 'cloned' nor 'installing tool dependencies'.
+        var tool_shed_repository_status_updater = function ( repository_status_list ) {
+            // See if there are any items left to track
+            var empty = true;
+            for ( i in repository_status_list ) {
+                empty = false;
+                break;
+            }
+            if ( ! empty ) {
+                setTimeout( function() { tool_shed_repository_status_updater_callback( repository_status_list ) }, 3000 );
+            }
+        };
+        var tool_shed_repository_status_updater_callback = function ( repository_status_list ) {
+            var ids = []
+            var status_list = []
+            $.each( repository_status_list, function ( id, repository_status ) {
+                ids.push( id );
+                status_list.push( repository_status );
+            });
+            // Make ajax call
+            $.ajax( {
+                type: "POST",
+                url: "${h.url_for( controller='admin_toolshed', action='repository_installation_status_updates' )}",
+                dataType: "json",
+                data: { id: ids[0], status_list: status_list.join( "," ) },
+                success : function ( data ) {
+                    $.each( data, function( id, val ) {
+                        // Replace HTML
+                        var cell1 = $("#RepositoryStatus-" + id);
+                        cell1.html( val.html_status );
+                        repository_status_list[ id ] = val.status;
+                    });
+                    tool_shed_repository_status_updater( repository_status_list ); 
+                },
+                error: function() {
+                    tool_shed_repository_status_updater( repository_status_list ); 
+                }
+            });
+        };
+    </script>
+</%def>
+
+<%def name="repository_installation_updater()">
+    <%
+        can_update = True
+        if tool_shed_repository:
+            can_update = tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.INSTALLED,
+                                                              trans.model.ToolShedRepository.installation_status.ERROR,
+                                                              trans.model.ToolShedRepository.installation_status.UNINSTALLED ]
+    %>
+    %if can_update:
+        <script type="text/javascript">
+            // Tool shed repository installation status updater
+            repository_installation_status_updater( {${ ",".join( [ '"%s" : "%s"' % ( trans.security.encode_id( repository.id ), repository.status ) for repository in query ] ) }});
+        </script>
+    %endif
+</%def>
+


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/confirm_tool_dependency_install.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/confirm_tool_dependency_install.mako
@@ -0,0 +1,86 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<% import os %>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="warningmessage">
+    <p>
+        The tool dependencies listed below can be automatically installed with the repository.  Installing them provides significant
+        benefits and Galaxy includes various features to manage them.
+    </p>
+    <p>
+        Each of these dependencies may require their own build requirements (e.g., CMake, g++, etc).  Galaxy will not attempt to install
+        these build requirements, so if any are missing from your environment tool dependency installation may partially fail.  The
+        repository and all of it's contents will be installed in any case.
+    </p>
+    <p>
+        If tool dependency installation fails in any way, you can install the missing build requirements and have Galaxy attempt to install
+        the tool dependencies again using the <b>Install tool dependencies</b> pop-up menu option on the <b>Manage repository</b> page.
+    </p> 
+</div>
+
+<div class="toolForm">
+    <div class="toolFormBody">
+        <form name="confirm_tool_dependency_install" id="confirm_tool_dependency_install" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, includes_tools=includes_tools )}" method="post" >
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Install tool dependencies?</label>
+                ${install_tool_dependencies_check_box.get_html()}
+                <div class="toolParamHelp" style="clear: both;">
+                    Un-check to skip automatic installation of these tool dependencies.
+                </div>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr>
+                    <tr>
+                        <th>Name</th>
+                        <th>Version</th>
+                        <th>Type</th>
+                        <th>Install directory</th>
+                    </tr>
+                    %for repository_name, repo_info_tuple in dict_with_tool_dependencies.items():
+                        <%
+                            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+                        %>
+                        %for dependency_key, requirements_dict in tool_dependencies.items():
+                            <%
+                                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 )
+                                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>${install_dir}</td>
+                                </tr>
+                                %if readme_text:
+                                    <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
+                                    <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
+                                %endif
+                            %endif
+                        %endfor
+                    %endfor
+                </table>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="confirm_tool_dependency_install_button" value="Continue"/>
+            </div>
+        </form>
+    </div>
+</div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -86,7 +86,7 @@
                         * The repository's installed tool dependencies will be removed from disk.
                     </div><div class="toolParamHelp" style="clear: both;">
-                        * Each associated tool dependency record's uninstalled column in the tool_dependency database table will be set to True.
+                        * Each associated tool dependency record's status column in the tool_dependency database table will be set to 'Uninstalled'.
                     </div>
                 %endif
                 %if repository.includes_datatypes:


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/install_missing_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/install_missing_tool_dependencies.mako
+++ /dev/null
@@ -1,109 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<% import os %>
-
-<br/><br/>
-<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">
-        <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="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
-        %if repository.includes_tools:
-            <a class="action-button" href="${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:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
-        %endif
-        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
-    </div>
-</ul>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="warningmessage">
-    <p>
-        Galaxy will attempt to install the missing tool dependencies listed below.  Each of these dependencies may require their own build
-        requirements (e.g., CMake, g++, etc).  Galaxy will not attempt to install these build requirements, so if any are missing from your
-        environment tool dependency installation may partially fail.  If this happens, you can install the missing build requirements and
-        have Galaxy attempt to install the tool dependencies again.
-    </p> 
-</div>
-<br/>
-<div class="warningmessage">
-    <p>
-        Installation may take a while.  <b>Always wait until a message is displayed in your browser after clicking the <b>Go</b> button below.</b>
-        If you get bored, watching your Galaxy server's paster log will help pass the time.
-    </p>
-    <p>
-        Information about the tool dependency installation process will be saved in various files named with a ".log" extension in the directory: 
-        ${trans.app.config.tool_dependency_dir}/<i>package name</i>/<i>package version</i>/${repository.owner}/${repository.name}/${repository.changeset_revision}
-    </p>
-</div>
-<br/>
-
-<div class="toolForm">
-    <div class="toolFormBody">
-        <form name="install_missing_tool_dependencies" id="install_missing_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ), tool_panel_section=tool_panel_section, new_tool_panel_section=new_tool_panel_section, reinstalling=reinstalling )}" method="post" >
-            <div style="clear: both"></div>
-            <div class="form-row">
-                <label>Install missing tool dependencies?</label>
-                ${install_tool_dependencies_check_box.get_html()}
-                <div class="toolParamHelp" style="clear: both;">
-                    Un-check to skip installation of these missing tool dependencies.
-                </div>
-                ## Fake the no_changes_check_box value.
-                %if no_changes_checked:
-                    <input type="hidden" id="no_changes" name="no_changes" value="true" checked="checked"><input type="hidden" name="no_changes" value="true">
-                %else:
-                    <input type="hidden" name="no_changes" value="true">
-                %endif
-            </div>
-            <div style="clear: both"></div>
-            <div class="form-row">
-                <table class="grid">
-                    <tr><td colspan="4" bgcolor="#D8D8D8"><b>Missing tool dependencies</b></td></tr>
-                    <tr>
-                        <th>Name</th>
-                        <th>Version</th>
-                        <th>Type</th>
-                        <th>Install directory</th>
-                    </tr>
-                    %for dependency_key, requirements_dict in tool_dependencies.items():
-                        <%
-                            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,
-                                                        repository.changeset_revision )
-                            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>${install_dir}</td>
-                            </tr>
-                            %if readme_text:
-                                <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
-                                <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
-                            %endif
-                        %endif
-                    %endfor
-                </table>
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <input type="submit" name="install_missing_tool_dependencies_button" value="Go"/>
-            </div>
-        </form>
-    </div>
-</div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/install_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/install_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/install_tool_dependencies.mako
@@ -25,16 +25,7 @@
 
 <div class="toolForm"><div class="toolFormBody">
-        <form name="install_tool_dependenceies" id="install_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, includes_tools=includes_tools )}" method="post" >
-            <div style="clear: both"></div>
-            <div class="form-row">
-                <label>Install tool dependencies?</label>
-                ${install_tool_dependencies_check_box.get_html()}
-                <div class="toolParamHelp" style="clear: both;">
-                    Un-check to skip automatic installation of these tool dependencies.
-                </div>
-            </div>
-            <div style="clear: both"></div>
+        <form name="install_tool_dependenceies" id="install_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies' )}" method="post" ><div class="form-row"><table class="grid"><tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr>
@@ -44,42 +35,46 @@
                         <th>Type</th><th>Install directory</th></tr>
-                    %for repository_name, repo_info_tuple in dict_with_tool_dependencies.items():
+                    <% tool_shed_repository = None %>
+                    %for tool_dependency in tool_dependencies:
+                        <input type="hidden" name="tool_dependency_ids" value="${trans.security.encode_id( tool_dependency.id )}"/><%
-                            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+                            readme_text = None
+                            if tool_shed_repository is None:
+                                tool_shed_repository = tool_dependency.tool_shed_repository
+                                metadata = tool_shed_repository.metadata
+                                tool_dependencies_dict = metadata[ 'tool_dependencies' ]
+                            for key, requirements_dict in tool_dependencies_dict.items():
+                                key_items = key.split( '/' )
+                                key_name = key_items[ 0 ]
+                                key_version = key_items[ 1 ]
+                                if key_name == tool_dependency.name and key_version == tool_dependency.version:
+                                    readme_text = requirements_dict.get( 'readme', None )
+                            install_dir = os.path.join( trans.app.config.tool_dependency_dir,
+                                                        tool_dependency.name,
+                                                        tool_dependency.version,
+                                                        tool_shed_repository.owner,
+                                                        tool_shed_repository.name,
+                                                        tool_shed_repository.installed_changeset_revision )
                         %>
-                        %for dependency_key, requirements_dict in tool_dependencies.items():
-                            <%
-                                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 )
-                                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>${install_dir}</td>
-                                </tr>
-                                %if readme_text:
-                                    <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
-                                    <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
-                                %endif
+                        %if not os.path.exists( install_dir ):
+                            <tr>
+                                <td>${tool_dependency.name}</td>
+                                <td>${tool_dependency.version}</td>
+                                <td>${tool_dependency.type}</td>
+                                <td>${install_dir}</td>
+                            </tr>
+                            %if readme_text:
+                                <tr><td colspan="4" bgcolor="#FFFFCC">${tool_dependency.name} ${tool_dependency.version} requirements and installation information</td></tr>
+                                <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
                             %endif
-                        %endfor
+                        %endif
                     %endfor
                 </table><div style="clear: both"></div></div><div class="form-row">
-                <input type="submit" name="install_tool_dependenceies_button" value="Continue"/>
+                <input type="submit" name="install_tool_dependencies_button" value="Install"/></div></form></div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -12,10 +12,8 @@
             <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a>
         %endif
         %if repository.tool_dependencies:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
-        %endif
-        %if repository.missing_tool_dependencies:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Install missing tool dependencies</a>
+            <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %>
+            <a class="action-button" href="${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="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a></div>
@@ -91,21 +89,15 @@
                         <td><b>version</b></td><td><b>type</b></td></tr>
-                    %for index, missing_dependency_tup in enumerate( missing_tool_dependencies ):
-                        <% name, version, type = missing_dependency_tup %>
+                    %for tool_dependency in missing_tool_dependencies:
                         <tr><td>
-                                <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="missing_dependency-${index}-popup">
-                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='install_tool_dependency', name=name, version=version, type=type, repository_id=trans.security.encode_id( repository.id ) )}">
-                                        ${name}
-                                    </a>
-                                </div>
-                                <div popupmenu="missing_dependency-${index}-popup">
-                                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_tool_dependency', name=name, version=version, type=type, repository_id=trans.security.encode_id( repository.id ) )}">Install this dependency</a>
-                                </div>
+                                <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.id ) )}">
+                                    ${tool_dependency.name}
+                                </a></td>
-                            <td>${version}</td>
-                            <td>${type}</td>
+                            <td>${tool_dependency.version}</td>
+                            <td>${tool_dependency.type}</td></tr>
                     %endfor
                 </table>
@@ -131,14 +123,9 @@
                     %for installed_tool_dependency in installed_tool_dependencies:
                         <tr><td>
-                                <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dependency-${installed_tool_dependency.id}-popup">
-                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
-                                        ${installed_tool_dependency.name}
-                                    </a>
-                                </div>
-                                <div popupmenu="dependency-${installed_tool_dependency.id}-popup">
-                                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">Uninstall this dependency</a>
-                                </div>
+                                <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
+                                    ${installed_tool_dependency.name}
+                                </a></td><td>${installed_tool_dependency.version}</td><td>${installed_tool_dependency.type}</td>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/manage_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/manage_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/manage_tool_dependencies.mako
@@ -13,9 +13,6 @@
         %if repository.includes_tools:
             <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a>
         %endif
-        %if repository.missing_tool_dependencies:
-            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Install missing tool dependencies</a>
-        %endif
         <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a></div></ul>
@@ -34,25 +31,25 @@
                         name = tool_dependency.name
                         version = tool_dependency.version
                         type = tool_dependency.type
-                        uninstalled = tool_dependency.uninstalled
+                        installed = tool_dependency.status == 'trans.model.ToolDependency.installation_status.INSTALLED
                         install_dir = tool_dependency.installation_directory( trans.app )
                     %><tr><td bgcolor="#D8D8D8"><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dependency-${tool_dependency.id}-popup">
-                                %if uninstalled:
-                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='install_tool_dependency', name=name, version=version, type=type, repository_id=trans.security.encode_id( repository.id ) )}">
+                                %if not installed:
+                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='browse', tool_dependency_id=trans.security.encode_id( tool_dependency.id ) )}"><b>Name</b></a><div popupmenu="dependency-${tool_dependency.id}-popup">
-                                        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_tool_dependency', name=name, version=version, type=type, repository_id=trans.security.encode_id( repository.id ) )}">Install this dependency</a>
+                                        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install', tool_dependency_id=trans.security.encode_id( tool_dependency.id ) )}">Install this tool dependency</a></div>
                                 %else:
-                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
+                                    <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='browse', tool_dependency_id=trans.security.encode_id( tool_dependency.id ) )}"><b>Name</b></a><div popupmenu="dependency-${tool_dependency.id}-popup">
-                                        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">Uninstall this dependency</a>
+                                        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='uninstall', tool_dependency_id=trans.security.encode_id( tool_dependency.id ) )}">Uninstall this tool dependency</a></div>
                                 %endif
                             </div>
@@ -64,7 +61,7 @@
                     <tr><th>Install directory</th><td>
-                            %if uninstalled:
+                            %if not installed:
                                 This dependency is not currently installed
                             %else:
                                 <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
@@ -73,7 +70,7 @@
                             %endif
                         </td></tr>
-                    <tr><th>Uninstalled</th><td>${uninstalled}</td></tr>
+                    <tr><th>Installed</th><td>${not installed}</td></tr>
                 %endfor
             </table><div style="clear: both"></div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -8,8 +8,9 @@
 <div class="toolForm"><div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div><div class="toolFormBody">
-        %if repository.includes_tool_dependencies:
-            <form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ), reinstalling=True )}" method="post" >
+        %if repository.tool_dependencies:
+            <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %>
+            <form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install', tool_dependency_ids=tool_dependency_ids )}" method="post" >
         %else:
             <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 ) )}" method="post" >
         %endif


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae 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
@@ -78,6 +78,7 @@
     <div class="toolForm"><div class="toolFormTitle">Repository README file (may contain important installation or license information)</div><div class="toolFormBody">
+            <input type="hidden" name="readme_text" value="${readme_text}"/><div class="form-row"><pre>${readme_text}</pre></div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/tool_dependencies_grid.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/tool_dependencies_grid.mako
@@ -0,0 +1,8 @@
+<%inherit file="/grid_base.mako"/>
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
+
+<%def name="javascripts()">
+   ${parent.javascripts()}
+   ${dependency_status_updater()}
+   ${tool_dependency_installation_updater()}
+</%def>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/tool_dependency_installation_status.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/tool_dependency_installation_status.mako
@@ -0,0 +1,13 @@
+<%def name="render_tool_dependency_status( tool_dependency )">
+    <%
+        if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLING:
+            bgcolor = trans.model.ToolDependency.states.INSTALLING
+            rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">' % ( bgcolor, trans.security.encode_id( tool_dependency.id ) )
+            rval += '%s</div>' % tool_dependency.status
+        else:
+            rval = tool_dependency.status
+    %>    
+    ${rval}
+</%def>
+
+${render_tool_dependency_status( tool_dependency )}


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
@@ -0,0 +1,52 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<% import os %>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Uninstall tool dependencies</div>
+    <div class="toolFormBody">
+        <form name="uninstall_tool_dependenceies" id="uninstall_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependencies' )}" method="post" >       
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <th>Name</th>
+                        <th>Version</th>
+                        <th>Type</th>
+                        <th>Install directory</th>
+                    </tr>
+                    %for tool_dependency in tool_dependencies:
+                        <input type="hidden" name="tool_dependency_ids" value="${trans.security.encode_id( tool_dependency.id )}"/>
+                        <%
+                            install_dir = os.path.join( trans.app.config.tool_dependency_dir,
+                                                        tool_dependency.name,
+                                                        tool_dependency.version,
+                                                        tool_dependency.tool_shed_repository.owner,
+                                                        tool_dependency.tool_shed_repository.name,
+                                                        tool_dependency.tool_shed_repository.installed_changeset_revision )
+                        %>
+                        %if os.path.exists( install_dir ):
+                            <tr>
+                                <td>${tool_dependency.name}</td>
+                                <td>${tool_dependency.version}</td>
+                                <td>${tool_dependency.type}</td>
+                                <td>${install_dir}</td>
+                            </tr>
+                        %endif
+                    %endfor
+                </table>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="uninstall_tool_dependencies_button" value="Uninstall"/>
+                <div class="toolParamHelp" style="clear: both;">
+                    Click to uninstall the tool dependencies listed above.
+                </div>
+            </div>
+        </form>
+    </div>
+</div>


diff -r a0a4f15fe0958c5ff2658c1695c63023b9cf6d39 -r db2bf800496478a5ea041480c3c514c2620e28ae templates/tool_form.mako
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -283,7 +283,7 @@
 %>
 
 %if tool_id_version_message:
-    ${render_msg( tool_id_version_message, 'error' )}
+    ${render_msg( tool_id_version_message, 'warning' )}
 %endif
 
 <div class="toolForm" id="${tool.id}">

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