Add the bx browser as a display app for builds hg18,hg19.mm8.mm9, and add the bx browser to the tool config for main.

lib/galaxy/config.py

@@ -81,6 +81,7 @@ class Configuration( object ):
         self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) )
         self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
         self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
+        self.bx_display_sites = kwargs.get( 'bx_display_sites', "main" ).lower().split(",")
         self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
         self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",")
         self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",")

lib/galaxy/datatypes/interval.py

@@ -54,6 +54,7 @@ class Interval( Tabular ):
         """Initialize interval datatype, by adding UCSC display apps"""
         Tabular.__init__(self, **kwd)
         self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' )
+        self.add_display_app ( 'main', 'BX', 'as_bx_display_file', 'bx_links' )
     
     def init_meta( self, dataset, copy_from=None ):
         Tabular.init_meta( self, dataset, copy_from=copy_from )
@@ -246,6 +247,29 @@ class Interval( Tabular ):
                         link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
                         ret_val.append( (site_name, link) )
         return ret_val
+    def bx_links( self, dataset, type, app, base_url ):
+        # TODO: abstract these methods to eliminate duplicate code.
+        ret_val = []
+        if dataset.has_data:
+            viewport_tuple = self.get_estimated_display_viewport(dataset)
+            if viewport_tuple:
+                chrom = viewport_tuple[0]
+                start = viewport_tuple[1]
+                stop = viewport_tuple[2]
+                for site_name, site_url in util.get_bx_by_build(dataset.dbkey):
+                    if site_name in app.config.bx_display_sites:
+                        # HACK: UCSC doesn't support https, so force http even
+                        # if our URL scheme is https.  Making this work
+                        # requires additional hackery in your upstream proxy.
+                        # If UCSC ever supports https, remove this hack.
+                        internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='bx_' + site_name )
+                        if base_url.startswith( 'https://' ):
+                            base_url = base_url.replace( 'https', 'http', 1 )
+                        display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
+                        redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
+                        link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
+                        ret_val.append( (site_name, link) )
+        return ret_val
 
     def validate( self, dataset ):
         """Validate an interval file using the bx GenomicIntervalReader"""

lib/galaxy/datatypes/tabular.py

@@ -214,6 +214,8 @@ class Tabular( data.Text ):
         return open( dataset.file_name )
     def as_ucsc_display_file( self, dataset, **kwd ):
         return open( dataset.file_name )
+    def as_bx_display_file( self, dataset, **kwd ):
+        return open( dataset.file_name )
 
 class Taxonomy( Tabular ):
     def __init__(self, **kwd):

lib/galaxy/util/__init__.py

@@ -278,7 +278,12 @@ def object_to_string( obj ):
 def string_to_object( s ):
     return pickle.loads( binascii.unhexlify( s ) )
         
-
+def get_bx_by_build(build):
+    sites = []
+    for site in bx_build_sites:
+        if build in site['builds']:
+            sites.append((site['name'],site['url']))
+    return sites
 def get_ucsc_by_build(build):
     sites = []
     for site in ucsc_build_sites:
@@ -471,6 +476,7 @@ def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
 galaxy_root_path = os.path.join(__path__[0], "..","..","..")
 # The dbnames list is used in edit attributes and the upload tool
 dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )
+bx_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "bx", "bx_build_sites.txt" ) )
 ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) )
 gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
 genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False )

tool-data/shared/bx/bx_build_sites.txt

@@ -0,0 +1 @@
+main	http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks?	hg18,hg19,mm8,mm9

tool_conf.xml.main

@@ -4,6 +4,7 @@
     <tool file="data_source/upload.xml"/>
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/bx_browser.xml" />
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/gramene_mart.xml" />

universe_wsgi.ini.sample

@@ -105,7 +105,8 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
 # Use the new iframe / javascript based layout
 use_new_layout = true
 
-# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing
+# Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing
+bx_display_sites = main
 ucsc_display_sites = main,test,archaea,ucla
 gbrowse_display_sites = main,test,tair
 # Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt