3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/edae5af34677/
Changeset: edae5af34677
Branch: release_15.03
User: dannon
Date: 2015-02-27 00:59:26+00:00
Summary: Fix server_starttime being in app for reports, toolshed. I will be
refactoring this shortly to have a base UniverseApplication from which things inherit.
Affected #: 2 files
diff -r 12a2f45243502295e324bf6656481a98c61101c0 -r
edae5af346776161c139666c33f15066f769cdb5 lib/galaxy/webapps/reports/app.py
--- a/lib/galaxy/webapps/reports/app.py
+++ b/lib/galaxy/webapps/reports/app.py
@@ -1,5 +1,7 @@
+import config
import sys
-import config
+import time
+
import galaxy.model
from galaxy.web import security
@@ -26,6 +28,8 @@
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
diff -r 12a2f45243502295e324bf6656481a98c61101c0 -r
edae5af346776161c139666c33f15066f769cdb5 lib/galaxy/webapps/tool_shed/app.py
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -1,17 +1,18 @@
import config
import sys
+import time
+import galaxy.datatypes.registry
+import galaxy.quota
+import galaxy.tools.data
+import galaxy.webapps.tool_shed.model
from galaxy import tools
-import galaxy.tools.data
-import galaxy.quota
-import galaxy.datatypes.registry
-import galaxy.webapps.tool_shed.model
+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 @@
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 ):
https://bitbucket.org/galaxy/galaxy-central/commits/be0aa5c296c7/
Changeset: be0aa5c296c7
Branch: release_15.03
User: dan
Date: 2015-02-27 20:50:13+00:00
Summary: Allow External display applications to use Tool Data Tables.
Affected #: 7 files
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -88,7 +88,7 @@
# 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
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1
lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -80,21 +80,57 @@
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 ) )
+ 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 = {}
- max_col = max( id_col, name_col )
+ 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 @@
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:
+ 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:
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 ) )
- else:
- log.warning( 'Invalid dynamic display application link specified
in %s: "%s"' % ( filename, line ) )
- self.links = rval
+ 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 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 @@
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 @@
# 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()
+
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1
lib/galaxy/datatypes/display_applications/parameters.py
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -59,7 +59,7 @@
@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
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -546,7 +546,7 @@
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 @@
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:
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1
lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
--- a/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
@@ -214,5 +214,5 @@
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 )
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -621,7 +621,7 @@
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.
diff -r edae5af346776161c139666c33f15066f769cdb5 -r
be0aa5c296c72e85dfea2effe7d228953ffcb8a1
lib/tool_shed/galaxy_install/tool_migration_manager.py
--- a/lib/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -523,7 +523,7 @@
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 ):
https://bitbucket.org/galaxy/galaxy-central/commits/fe4cfbd300a1/
Changeset: fe4cfbd300a1
Branch: release_15.03
User: dan
Date: 2015-02-27 20:50:28+00:00
Summary: Have IGV external display application load a set of links for available
genomes via a tool data table that reads a URL
(
http://igv.broadinstitute.org/genomes/genomes.txt). The manually specified builds links
should now be used to add additional builds, or for alias mapping (e.g.
hg_g1k_v37-->b37).
Affected #: 4 files
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r
fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 config/tool_data_table_conf.xml.sample
--- a/config/tool_data_table_conf.xml.sample
+++ b/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>
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r
fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/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?session...
$bam_file.name )}</url>
+
+ <param type="data" name="bam_file"
url="galaxy_${DATASET_HASH}.bam" />
+ <param type="data" name="bai_file"
url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+
+ </dynamic_links></display><!-- Dan Blankenberg -->
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r
fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -93,7 +93,20 @@
#end if
</param></dynamic_links>
-
+
+
+ <dynamic_links from_data_table="igv_broad_genomes"
skip_startswith="#" id="value" name="name">
+
+ <!-- Our input data table is one line per dbkey -->
+ <filter>${ $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?session...
$bgzip_file.name )}</url>
+
+ <param type="data" name="bgzip_file"
url="galaxy_${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 -->
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r
fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 tool-data/shared/igv/igv_build_sites.txt.sample
--- a/tool-data/shared/igv/igv_build_sites.txt.sample
+++ b/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
\ No newline at end of file
+#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
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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