Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03

config/datatypes_conf.xml.sample

@@ -180,7 +180,7 @@
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension.  You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
     <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
     <datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="True"/>
-    <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.txt:SnpSiftDbNSFP" display_in_upload="True"/>
+    <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="True"/>
     <datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True">
         <converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/>
     </datatype>

config/tool_data_table_conf.xml.sample

@@ -65,4 +65,9 @@
         <columns>value, path</columns>
         <file path="tool-data/twobit.loc" />
     </table>
+    <!-- Available IGV builds, loaded from URL -->
+    <table name="igv_broad_genomes" comment_char="#">
+        <columns>name, url, value</columns>
+        <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
+    </table>
 </tables>

display_applications/igv/bam.xml

@@ -93,7 +93,20 @@
             #end if
         </param>
     </dynamic_links>
-    
+
+
+    <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+        <!-- Our input data table is one line per dbkey -->
+        <filter>${ $dataset.dbkey == $value }</filter>
+
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&amp;genome=${bam_file.dbkey}&amp;merge=true&amp;name=${qp( $bam_file.name )}</url>
+
+        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+
+    </dynamic_links>
     
 </display>
 <!-- Dan Blankenberg -->

display_applications/igv/vcf.xml

@@ -93,7 +93,20 @@
             #end if
         </param>
     </dynamic_links>
-    
+
+
+    <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+        <!-- Our input data table is one line per dbkey -->
+        <filter>${ $dataset.dbkey == $value }</filter>
+
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=$bgzip_file.dbkey&amp;merge=true&amp;name=${qp( $bgzip_file.name )}</url>
+
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+
+    </dynamic_links>
     
 </display>
 <!-- Dan Blankenberg -->

lib/galaxy/app.py

@@ -88,7 +88,7 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
         # Load proprietary datatype converters and display applications.
         self.installed_repository_manager.load_proprietary_converters_and_display_applications()
         # Load datatype display applications defined in local datatypes_conf.xml
-        self.datatypes_registry.load_display_applications()
+        self.datatypes_registry.load_display_applications( self )
         # Load datatype converters defined in local datatypes_conf.xml
         self.datatypes_registry.load_datatype_converters( self.toolbox )
         # Load external metadata tool

lib/galaxy/datatypes/display_applications/application.py

@@ -80,21 +80,57 @@ class DisplayApplicationLink( object ):
         return True
 
 class DynamicDisplayApplicationBuilder( object ):
-    @classmethod
+
     def __init__( self, elem, display_application, build_sites ):
-        rval = []
         filename = None
+        data_table = None
         if elem.get( 'site_type', None ) is not None:
             filename = build_sites.get( elem.get( 'site_type' ) )
         else:
             filename = elem.get( 'from_file', None )
-        assert filename is not None, 'Filename and id attributes required for dynamic_links'
+        if filename is None:
+            data_table_name = elem.get( 'from_data_table', None )
+            if data_table_name:
+                data_table = display_application.app.tool_data_tables.get( data_table_name, None )
+                assert data_table is not None, 'Unable to find data table named "%s".' % data_table_name
+        
+        assert filename is not None or data_table is not None,'Filename or data Table is required for dynamic_links.'
         skip_startswith = elem.get( 'skip_startswith', None )
         separator = elem.get( 'separator', '\t' )
-        id_col = int( elem.get( 'id', None ) )
-        name_col = int( elem.get( 'name', id_col ) )
-        dynamic_params = {}
+        id_col = elem.get( 'id', None )
+        try:
+            id_col = int( id_col )
+        except:
+            if data_table:
+                if id_col is None:
+                    id_col = data_table.columns.get( 'id', None )
+                if id_col is None:
+                    id_col = data_table.columns.get( 'value', None )
+                try:
+                    id_col = int( id_col )
+                except:
+                    # id is set to a string or None, use column by that name if available
+                    id_col = data_table.columns.get( id_col, None )
+                    id_col = int( id_col )
+        name_col = elem.get( 'name', None )
+        try:
+            name_col = int( name_col )
+        except:
+            if data_table:
+                if name_col is None:
+                    name_col = data_table.columns.get( 'name', None )
+                else:
+                    name_col = data_table.columns.get( name_col, None )
+            else:
+                name_col = None
+        if name_col is None:
+            name_col = id_col
         max_col = max( id_col, name_col )
+        dynamic_params = {}
+        if data_table is not None:
+            max_col = max(  [ max_col ] + data_table.columns.values() )
+            for key, value in data_table.columns.items():
+                dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
         for dynamic_param in elem.findall( 'dynamic_param' ):
             name = dynamic_param.get( 'name' )
             value = int( dynamic_param.get( 'value' ) )
@@ -102,27 +138,38 @@ class DynamicDisplayApplicationBuilder( object ):
             param_separator =  dynamic_param.get( 'separator', ',' )
             max_col = max( max_col, value )
             dynamic_params[name] = { 'column': value, 'split': split, 'separator': param_separator }
-        for line in open( filename ):
-            if not skip_startswith or not line.startswith( skip_startswith ):
-                line = line.rstrip( '\n\r' )
-                if not line:
-                    continue
-                fields = line.split( separator )
-                if len( fields ) > max_col:
-                    new_elem = deepcopy( elem )
-                    new_elem.set( 'id', fields[id_col] )
-                    new_elem.set( 'name', fields[name_col] )
-                    dynamic_values = {}
-                    for key, attributes in dynamic_params.iteritems():
-                        value = fields[ attributes[ 'column' ] ]
-                        if attributes['split']:
-                            value = value.split( attributes['separator'] )
-                        dynamic_values[key] = value
-                    #now populate
-                    rval.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
+        if filename:
+            data_iter = open( filename )
+        elif data_table:
+            version, data_iter = data_table.get_version_fields()
+            display_application.add_data_table_watch( data_table.name, version )
+        links = []
+        for line in data_iter:
+            if isinstance( line, basestring ):
+                if not skip_startswith or not line.startswith( skip_startswith ):
+                    line = line.rstrip( '\n\r' )
+                    if not line:
+                        continue
+                    fields = line.split( separator )
                 else:
-                    log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
-        self.links = rval
+                    continue
+            else:
+                fields = line
+            if len( fields ) > max_col:
+                new_elem = deepcopy( elem )
+                new_elem.set( 'id', fields[id_col] )
+                new_elem.set( 'name', fields[name_col] )
+                dynamic_values = {}
+                for key, attributes in dynamic_params.iteritems():
+                    value = fields[ attributes[ 'column' ] ]
+                    if attributes['split']:
+                        value = value.split( attributes['separator'] )
+                    dynamic_values[key] = value
+                #now populate
+                links.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
+            else:
+                log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
+        self.links = links
     def __iter__( self ):
         return iter( self.links )
 
@@ -166,12 +213,12 @@ class PopulatedDisplayApplicationLink( object ):
 
 class DisplayApplication( object ):
     @classmethod
-    def from_file( cls, filename, datatypes_registry ):
-        return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry, filename=filename )
+    def from_file( cls, filename, app ):
+        return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename )
     @classmethod
-    def from_elem( cls, elem, datatypes_registry, filename=None ):
+    def from_elem( cls, elem, app, filename=None ):
         att_dict = cls._get_attributes_from_elem( elem )
-        rval = DisplayApplication( att_dict['id'], att_dict['name'], datatypes_registry, att_dict['version'], filename=filename, elem=elem )
+        rval = DisplayApplication( att_dict['id'], att_dict['name'], app, att_dict['version'], filename=filename, elem=elem )
         rval._load_links_from_elem( elem )
         return rval
     @classmethod
@@ -181,29 +228,32 @@ class DisplayApplication( object ):
         name = elem.get( 'name', display_id )
         version = elem.get( 'version', None )
         return dict( id=display_id, name=name, version=version )
-    def __init__( self, display_id, name, datatypes_registry, version = None, filename=None, elem=None ):
+    def __init__( self, display_id, name, app, version = None, filename=None, elem=None ):
         self.id = display_id
         self.name = name
-        self.datatypes_registry = datatypes_registry
+        self.app = app
         if version is None:
             version = "1.0.0"
         self.version = version
         self.links = odict()
         self._filename = filename
         self._elem = elem
+        self._data_table_versions = {}
     def _load_links_from_elem( self, elem ):
         for link_elem in elem.findall( 'link' ):
             link = DisplayApplicationLink.from_elem( link_elem, self )
             if link:
                 self.links[ link.id ] = link
         for dynamic_links in elem.findall( 'dynamic_links' ):
-            for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.datatypes_registry.build_sites ):
+            for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
                 self.links[ link.id ] = link
     def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
         #returns a link object with data knowledge to generate links
+        self._check_and_reload()
         return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans, app_kwds )
     def filter_by_dataset( self, data, trans ):
-        filtered = DisplayApplication( self.id, self.name, self.datatypes_registry, version = self.version )
+        self._check_and_reload()
+        filtered = DisplayApplication( self.id, self.name, self.app, version = self.version )
         for link_name, link_value in self.links.iteritems():
             if link_value.filter_by_dataset( data, trans ):
                 filtered.links[link_name] = link_value
@@ -222,9 +272,24 @@ class DisplayApplication( object ):
         # clear old links
         for key in self.links.keys():
             del self.links[key]
+        #clear data table versions:
+        for key in self._data_table_versions.keys():
+            del self._data_table_versions[ key ]
         # Set new attributes
         for key, value in attr_dict.iteritems():
             setattr( self, key, value )
         # Load new links
         self._load_links_from_elem( elem )
         return self
+    def add_data_table_watch( self, table_name, version=None ):
+        self._data_table_versions[ table_name ] = version
+    def _requires_reload( self ):
+        for key, value in self._data_table_versions.iteritems():
+            table = self.app.tool_data_tables.get( key, None )
+            if table and not table.is_current_version( value ):
+                return True
+        return False
+    def _check_and_reload( self ):
+        if self._requires_reload():
+            self.reload()
+

lib/galaxy/datatypes/display_applications/parameters.py

@@ -59,7 +59,7 @@ class DisplayApplicationDataParameter( DisplayApplicationParameter ):
     @property
     def formats( self ):
         if self.extensions:
-            return tuple( map( type, map( self.link.display_application.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
+            return tuple( map( type, map( self.link.display_application.app.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
         return None
     def _get_dataset_like_object( self, other_values ):
         #this returned object has file_name, state, and states attributes equivalent to a DatasetAssociation

lib/galaxy/datatypes/registry.py

@@ -546,7 +546,7 @@ class Registry( object ):
                 else:
                     self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) )
 
-    def load_display_applications( self, installed_repository_dict=None, deactivate=False ):
+    def load_display_applications( self, app, installed_repository_dict=None, deactivate=False ):
         """
         If deactivate is False, add display applications from self.display_app_containers or
         self.proprietary_display_app_containers to appropriate datatypes.  If deactivate is
@@ -570,7 +570,7 @@ class Registry( object ):
                     config_path = os.path.join( self.display_applications_path, display_file )
                 try:
                     inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) )
-                    display_app = DisplayApplication.from_file( config_path, self )
+                    display_app = DisplayApplication.from_file( config_path, app )
                     if display_app:
                         if display_app.id in self.display_applications:
                             if deactivate:

lib/galaxy/webapps/reports/app.py

@@ -1,5 +1,7 @@
-import sys
 import config
+import sys
+import time
+
 import galaxy.model
 from galaxy.web import security
 
@@ -26,6 +28,8 @@ class UniverseApplication( object ):
         self.targets_mysql = 'mysql' in self.config.database_connection
         # Security helper
         self.security = security.SecurityHelper( id_secret=self.config.id_secret )
+        # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
+        self.server_starttime = int(time.time())
 
     def shutdown( self ):
         pass

lib/galaxy/webapps/tool_shed/app.py

@@ -1,17 +1,18 @@
 import config
 import sys
-from galaxy import tools
-import galaxy.tools.data
-import galaxy.quota
+import time
 import galaxy.datatypes.registry
+import galaxy.quota
+import galaxy.tools.data
 import galaxy.webapps.tool_shed.model
+from galaxy import tools
+from galaxy.managers.tags import CommunityTagManager
 from galaxy.openid.providers import OpenIDProviders
 from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web import security
-from galaxy.managers.tags import CommunityTagManager
-from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
 import tool_shed.repository_registry
 import tool_shed.repository_types.registry
+from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
 
 
 class UniverseApplication( object ):
@@ -70,6 +71,8 @@ class UniverseApplication( object ):
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         # Initialize the repository registry.
         self.repository_registry = tool_shed.repository_registry.Registry( self )
+        #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
+        self.server_starttime = int(time.time())
         print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
 
     def shutdown( self ):

lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py

@@ -214,5 +214,5 @@ class CustomDatatypeLoader( object ):
 
     def load_installed_display_applications( self, installed_repository_dict, deactivate=False ):
         """Load or deactivate custom datatype display applications."""
-        self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict,
+        self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=installed_repository_dict,
                                                                deactivate=deactivate )

lib/tool_shed/galaxy_install/install_manager.py

@@ -621,7 +621,7 @@ class InstallRepositoryManager( object ):
                 self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict )
             if display_path:
                 # Load proprietary datatype display applications
-                self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+                self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
 
     def handle_tool_shed_repositories( self, installation_dict, using_api=False ):
         # The following installation_dict entries are all required.

lib/tool_shed/galaxy_install/tool_migration_manager.py

@@ -523,7 +523,7 @@ class ToolMigrationManager( object ):
                                                                       installed_repository_dict=repository_dict )
             if display_path:
                 # Load proprietary datatype display applications
-                self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+                self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
             basic_util.remove_dir( work_dir )
 
     def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):

tool-data/shared/igv/igv_build_sites.txt.sample

@@ -1,4 +1,4 @@
 #site_id	site_name	site_url	dbkey	ivg_build_name
-web_link_main	web current	http://www.broadinstitute.org/igv/projects/current/igv.php	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+web_link_main	web current	http://www.broadinstitute.org/igv/projects/current/igv.php	hg_g1k_v37	b37
 #web_jnlp_1.5	web 1.5	http://www.broadinstitute.org/igvdata/jws/prod	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
-#local_default	local	http://localhost:60151/load	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+#local_default	local	http://localhost:60151/load	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum