Merge

datatypes_conf.xml.sample

@@ -169,7 +169,6 @@
     <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
     <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
-    <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
       <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
@@ -246,7 +245,6 @@
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:Bam"/>
     <sniffer type="galaxy.datatypes.binary:Sff"/>
-    <sniffer type="galaxy.datatypes.xml:BlastXml"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.sequence:Maf"/>
     <sniffer type="galaxy.datatypes.sequence:Lav"/>

lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true">
+  <!-- Used internally to generate track indexes -->
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
+  <inputs>
+    <page>
+      <param format="bedgraph" name="input" type="data" label="Choose wiggle"/>
+    </page>
+   </inputs>
+   <outputs>
+      <data format="bigwig" name="output"/>
+   </outputs>
+  <help>
+  </help>
+</tool>

lib/galaxy/datatypes/converters/gff_to_fli.py

@@ -6,48 +6,52 @@ import sys
 from galaxy import eggs
 from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed
 
-# Process arguments.
-in_fname = sys.argv[1]
-out_fname = sys.argv[2]
+def main():
+    # Process arguments.
+    in_fname = sys.argv[1]
+    out_fname = sys.argv[2]
+    
+    # Create dict of name-location pairings.
+    name_loc_dict = {}
+    for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
+        for name in feature.attributes:
+            val = feature.attributes[ name ]
+            try:
+                float( val )
+                continue
+            except:
+                convert_gff_coords_to_bed( feature )
+                # Value is not a number, so it can be indexed.
+                if val not in name_loc_dict:
+                    # Value is not in dictionary.
+                    name_loc_dict[ val ] = {
+                        'contig': feature.chrom,
+                        'start': feature.start,
+                        'end': feature.end
+                    }
+                else:
+                    # Value already in dictionary, so update dictionary.
+                    loc = name_loc_dict[ val ]
+                    if feature.start < loc[ 'start' ]:
+                        loc[ 'start' ] = feature.start
+                    if feature.end > loc[ 'end' ]:
+                        loc[ 'end' ] = feature.end
+    
+    # Print name, loc in sorted order.
+    out = open( out_fname, 'w' )
+    max_len = 0
+    entries = []
+    for name in sorted( name_loc_dict.iterkeys() ):
+        loc = name_loc_dict[ name ]
+        entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
+        if len( entry ) > max_len:
+            max_len = len( entry )
+        entries.append( entry )
+        
+    out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
+    for entry in entries:
+        out.write( entry.ljust( max_len ) + '\n' )
+    out.close()
 
-# Create dict of name-location pairings.
-name_loc_dict = {}
-for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
-	for name in feature.attributes:
-		val = feature.attributes[ name ]
-		try:
-			float( val )
-			continue
-		except:
-			convert_gff_coords_to_bed( feature )
-			# Value is not a number, so it can be indexed.
-			if val not in name_loc_dict:
-				# Value is not in dictionary.
-				name_loc_dict[ val ] = {
-					'contig': feature.chrom,
-					'start': feature.start,
-					'end': feature.end
-				}
-			else:
-				# Value already in dictionary, so update dictionary.
-				loc = name_loc_dict[ val ]
-				if feature.start < loc[ 'start' ]:
-					loc[ 'start' ] = feature.start
-				if feature.end > loc[ 'end' ]:
-					loc[ 'end' ] = feature.end
-
-# Print name, loc in sorted order.
-out = open( out_fname, 'w' )
-max_len = 0
-entries = []
-for name in sorted( name_loc_dict.iterkeys() ):
-	loc = name_loc_dict[ name ]
-	entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
-	if len( entry ) > max_len:
-		max_len = len( entry )
-	entries.append( entry )
-	
-out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
-for entry in entries:
-	out.write( entry.ljust( max_len ) + '\n' )
-out.close()
+if __name__ == '__main__':
+    main()

lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py.orig

@@ -1,79 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from interval file to interval index file. Default input file format is BED (0-based, half-open intervals).
-
-usage: %prog in_file out_file
-    -G, --gff: input is GFF format, meaning start and end coordinates are 1-based, closed interval
-"""
-
-from __future__ import division
-
-import sys, fileinput
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from galaxy.visualization.tracks.summary import *
-from bx.cookbook import doc_optparse
-from galaxy.tools.util.gff_util import convert_gff_coords_to_bed
-from bx.interval_index_file import Indexes
-from galaxy.tools.util.gff_util import parse_gff_attributes
-
-def main():
-    
-    # Read options, args.
-    options, args = doc_optparse.parse( __doc__ )
-    try:
-        gff_format = bool( options.gff )
-        input_fname, out_fname = args
-    except:
-        doc_optparse.exception()
-    
-    # Do conversion.
-    # TODO: take column numbers from command line.
-    if gff_format:
-        chr_col, start_col, end_col = ( 0, 3, 4 )
-    else:
-        chr_col, start_col, end_col = ( 0, 1, 2 )
-    index = Indexes()
-    offset = 0
-    # Need to keep track of last gene, transcript id for indexing GTF files.
-    last_gene_id = None
-    last_transcript_id = None
-    for line in open(input_fname, "r"):
-        feature = line.strip().split('\t')
-        if not feature or feature[0].startswith("track") or feature[0].startswith("#"):
-            offset += len(line)
-            continue
-        chrom = feature[ chr_col ]
-        chrom_start = int( feature[ start_col ] )
-        chrom_end = int( feature[ end_col ] )
-        if gff_format:
-            chrom_start, chrom_end = convert_gff_coords_to_bed( [chrom_start, chrom_end ] )
-            
-            # Only add feature if gene_id, transcript_id are different from last 
-            # values.
-            if len( feature ) == 9:
-                attributes = parse_gff_attributes( feature[8] )
-                gene_id = attributes.get( 'gene_id', None )
-                transcript_id = attributes.get( 'transcript_id', None )
-                if gene_id and transcript_id and gene_id == last_gene_id and \
-                   transcript_id == last_transcript_id:
-                    # Feature has same gene_id, transcript as last feature, so 
-                    # do not add.
-                    offset += len(line)
-                    continue
-                else:
-                    # gene_id, transcript_id set and are different from last 
-                    # values.
-                    last_gene_id = gene_id
-                    last_transcript_id = transcript_id
-
-        #print "%s %s %s %s %i %i %i" % (feature[2], last_gene_id, last_transcript_id, chrom, chrom_start, chrom_end, offset)
-        index.add( chrom, chrom_start, chrom_end, offset )
-        offset += len(line)
-            
-    index.write( open(out_fname, "w") )
-
-if __name__ == "__main__": 
-    main()
-    

lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml

@@ -1,6 +1,6 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command>wigToBigWig $input $chromInfo $output</command>
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
   <inputs>
     <page>
       <param format="wig" name="input" type="data" label="Choose wiggle"/>

lib/galaxy/datatypes/interval.py

@@ -338,7 +338,7 @@ class BedGraph( Interval ):
     file_ext = "bedgraph"
 
     def get_track_type( self ):
-        return "LineTrack", {"data": "array_tree"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
         
     def as_ucsc_display_file( self, dataset, **kwd ):
         """
@@ -1141,8 +1141,9 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         resolution = min( resolution, 100000 )
         resolution = max( resolution, 1 )
         return resolution
+        
     def get_track_type( self ):
-        return "LineTrack", {"data": "bigwig", "index": "bigwig"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
 
 class CustomTrack ( Tabular ):
     """UCSC CustomTrack"""

lib/galaxy/datatypes/registry.py

@@ -276,7 +276,6 @@ class Registry( object ):
                 'axt'         : sequence.Axt(),
                 'bam'         : binary.Bam(),
                 'bed'         : interval.Bed(), 
-                'blastxml'    : xml.BlastXml(),
                 'coverage'    : coverage.LastzCoverage(),
                 'customtrack' : interval.CustomTrack(),
                 'csfasta'     : sequence.csFasta(),
@@ -310,7 +309,6 @@ class Registry( object ):
                 'axt'         : 'text/plain',
                 'bam'         : 'application/octet-stream',
                 'bed'         : 'text/plain', 
-                'blastxml'    : 'application/xml', 
                 'customtrack' : 'text/plain',
                 'csfasta'     : 'text/plain',
                 'eland'       : 'application/octet-stream',
@@ -348,7 +346,6 @@ class Registry( object ):
             self.sniff_order = [
                 binary.Bam(),
                 binary.Sff(),
-                xml.BlastXml(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),

lib/galaxy/datatypes/tabular.py

@@ -264,10 +264,10 @@ class Tabular( data.Text ):
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
         #TODO Prevent failure when displaying extremely long > 50kb lines.
-        if to_ext or not preview:
-            return self._serve_raw(trans, dataset, to_ext)
         if chunk:
             return self.get_chunk(trans, dataset, chunk)
+        if to_ext or not preview:
+            return self._serve_raw(trans, dataset, to_ext)
         else:
             column_names = 'null'
             if dataset.metadata.column_names:
@@ -644,4 +644,5 @@ class FeatureLocationIndex( Tabular ):
     """
     file_ext='fli'
     MetadataElement( name="columns", default=2, desc="Number of columns", readonly=True, visible=False )
-    MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
+    MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
+

lib/galaxy/datatypes/xml.py

@@ -27,9 +27,6 @@ class GenericXml( data.Text ):
         >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
         >>> GenericXml().sniff( fname )
         True
-        >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
-        >>> BlastXml().sniff( fname )
-        True
         >>> fname = get_test_fname( 'interval.interval' )
         >>> GenericXml().sniff( fname )
         False
@@ -50,123 +47,6 @@ class GenericXml( data.Text ):
         data.Text.merge(split_files, output_file)
     merge = staticmethod(merge)
 
-class BlastXml( GenericXml ):
-    """NCBI Blast XML Output data"""
-    file_ext = "blastxml"
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        """Set the peek and blurb text"""
-        if not dataset.dataset.purged:
-            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            dataset.blurb = 'NCBI Blast XML data'
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def sniff( self, filename ):
-        """
-        Determines whether the file is blastxml
-        
-        >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
-        >>> BlastXml().sniff( fname )
-        True
-        >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
-        >>> BlastXml().sniff( fname )
-        True
-        >>> fname = get_test_fname( 'interval.interval' )
-        >>> BlastXml().sniff( fname )
-        False
-        """
-        #TODO - Use a context manager on Python 2.5+ to close handle
-        handle = open(filename)
-        line = handle.readline()
-        if line.strip() != '<?xml version="1.0"?>':
-            handle.close()
-            return False
-        line = handle.readline()
-        if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
-            handle.close()
-            return False
-        line = handle.readline()
-        if line.strip() != '<BlastOutput>':
-            handle.close()
-            return False
-        handle.close()
-        return True
-    
-    def merge(split_files, output_file):
-        """Merging multiple XML files is non-trivial and must be done in subclasses."""
-        if len(split_files) == 1:
-            #For one file only, use base class method (move/copy)
-            return data.Text.merge(split_files, output_file)
-        out = open(output_file, "w")
-        h = None
-        for f in split_files:
-            h = open(f)
-            body = False
-            header = h.readline()
-            if not header:
-                out.close()
-                h.close()
-                raise ValueError("BLAST XML file %s was empty" % f)
-            if header.strip() != '<?xml version="1.0"?>':
-                out.write(header) #for diagnosis
-                out.close()
-                h.close()
-                raise ValueError("%s is not an XML file!" % f)
-            line = h.readline()
-            header += line
-            if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                    '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
-                out.write(header) #for diagnosis
-                out.close()
-                h.close()
-                raise ValueError("%s is not a BLAST XML file!" % f)
-            while True:
-                line = h.readline()
-                if not line:
-                    out.write(header) #for diagnosis
-                    out.close()
-                    h.close()
-                    raise ValueError("BLAST XML file %s ended prematurely" % f)
-                header += line
-                if "<Iteration>" in line:
-                    break
-                if len(header) > 10000:
-                    #Something has gone wrong, don't load too much into memory!
-                    #Write what we have to the merged file for diagnostics
-                    out.write(header)
-                    out.close()
-                    h.close()
-                    raise ValueError("BLAST XML file %s has too long a header!" % f)
-            if "<BlastOutput>" not in header:
-                out.close()
-                h.close()
-                raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
-            if f == split_files[0]:
-                out.write(header)
-                old_header = header
-            elif old_header[:300] != header[:300]:
-                #Enough to check <BlastOutput_program> and <BlastOutput_version> match
-                out.close()
-                h.close()
-                raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
-                                 % (split_files[0], f, old_header[:300], header[:300]))
-            else:
-                out.write("    <Iteration>\n")
-            for line in h:
-                if "</BlastOutput_iterations>" in line:
-                    break
-                #TODO - Increment <Iteration_iter-num> and if required automatic query names
-                #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
-                out.write(line)
-            h.close()
-        out.write("  </BlastOutput_iterations>\n")
-        out.write("</BlastOutput>\n")
-        out.close()
-    merge = staticmethod(merge)
-                                                
-
 class MEMEXml( GenericXml ):
     """MEME XML Output data"""
     file_ext = "memexml"

lib/galaxy/jobs/__init__.py

@@ -490,7 +490,6 @@ class JobWrapper( object ):
         if stderr contains anything, then False is returned.
         Note that the job id is just for messages.
         """
-        err_msg = ""
         # By default, the tool succeeded. This covers the case where the code 
         # has a bug but the tool was ok, and it lets a workflow continue.
         success = True 
@@ -507,7 +506,7 @@ class JobWrapper( object ):
                 # Check the exit code ranges in the order in which
                 # they were specified. Each exit_code is a StdioExitCode
                 # that includes an applicable range. If the exit code was in
-                # that range, then apply the error level and add in a message.
+                # that range, then apply the error level and add a message.
                 # If we've reached a fatal error rule, then stop.
                 max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR
                 for stdio_exit_code in self.tool.stdio_exit_codes:
@@ -515,20 +514,16 @@ class JobWrapper( object ):
                          tool_exit_code <= stdio_exit_code.range_end ):
                         # Tack on a generic description of the code 
                         # plus a specific code description. For example,
-                        # this might append "Job 42: Warning: Out of Memory\n".
-                        # TODO: Find somewhere to stick the err_msg - 
-                        # possibly to the source (stderr/stdout), possibly 
-                        # in a new db column.
+                        # this might prepend "Job 42: Warning: Out of Memory\n".
                         code_desc = stdio_exit_code.desc
                         if ( None == code_desc ):
                             code_desc = ""
-                        tool_msg = ( "Job %s: %s: Exit code %d: %s" % (
-                                     job.get_id_tag(),
-                                     galaxy.tools.StdioErrorLevel.desc( tool_exit_code ),
+                        tool_msg = ( "%s: Exit code %d: %s" % (
+                                     galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ),
                                      tool_exit_code,
                                      code_desc ) )
-                        log.info( tool_msg )
-                        stderr = err_msg + stderr
+                        log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) )
+                        stderr = tool_msg + "\n" + stderr
                         max_error_level = max( max_error_level, 
                                                stdio_exit_code.error_level )
                         if ( max_error_level >= 
@@ -571,7 +566,6 @@ class JobWrapper( object ):
                                                      re.IGNORECASE )
                             if ( regex_match ):
                                 rexmsg = self.regex_err_msg( regex_match, regex)
-                                # DELETEME
                                 log.info( "Job %s: %s" 
                                         % ( job.get_id_tag(), rexmsg ) )
                                 stderr = rexmsg + "\n" + stderr

lib/galaxy/tool_shed/migrate/versions/0004_tools.py

@@ -0,0 +1,14 @@
+"""
+The NCBI BLAST+ tools have been eliminated from the distribution.  The tools and
+datatypes are are now available in repositories named ncbi_blast_plus and
+blast_datatypes, respectively, from the main Galaxy tool shed at
+http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance
+at the location discussed above by running the following command.
+"""
+
+import sys
+
+def upgrade():
+    print __doc__
+def downgrade():
+    pass

lib/galaxy/tools/__init__.py

@@ -2631,7 +2631,7 @@ class Tool:
         if for_link:
             # Create tool link.
             if not self.tool_type.startswith( 'data_source' ):
-                link = url_for( controller='tool_runner', tool_id=self.id )
+                link = url_for( '/tool_runner', tool_id=self.id )
             else:
                 link = url_for( self.action, **self.get_static_param_values( trans ) )
             

lib/galaxy/visualization/tracks/data_providers.py

@@ -968,29 +968,32 @@ class BBIDataProvider( TracksDataProvider ):
         # which we use converted_dataset
         f, bbi = self._get_dataset()
        
-        # If the stats kwarg was provide, we compute overall summary data for the 
-        # range defined by start and end but no reduced data. This is currently 
-        # used by client to determine the default range.
+        # If stats requested, compute overall summary data for the range
+        # start:endbut no reduced data. This is currently used by client 
+        # to determine the default range.
         if 'stats' in kwargs:
             summary = bbi.summarize( chrom, start, end, 1 )
             f.close()
-            if summary is None:
-                return None
-            else:
+            
+            min = 0
+            max = 0
+            mean = 0
+            sd = 0
+            if summary is not None:
                 # Does the summary contain any defined values?
                 valid_count = summary.valid_count[0]
-                if summary.valid_count < 1:
-                    return None
+                if summary.valid_count > 0:
+                    # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower
+                    # bounds that contain ~95% of the data.
+                    mean = summary.sum_data[0] / valid_count
+                    var = summary.sum_squares[0] - mean
+                    if valid_count > 1:
+                        var /= valid_count - 1
+                    sd = numpy.sqrt( var )
+                    min = summary.min_val[0]
+                    max = summary.max_val[0]
 
-                # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower
-                # bounds that contain ~95% of the data.
-                mean = summary.sum_data[0] / valid_count
-                var = summary.sum_squares[0] - mean
-                if valid_count > 1:
-                    var /= valid_count - 1
-                sd = numpy.sqrt( var )
-
-                return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
+            return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) )
 
         # Sample from region using approximately this many samples.
         N = 1000

lib/galaxy/web/controllers/tracks.py

@@ -387,7 +387,21 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
             return return_message
             
         extra_info = None
-        if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and kwargs.get("mode", "Auto") == "Auto":
+        mode = kwargs.get( "mode", "Auto" )
+        # Handle histogram mode uniquely for now:
+        if mode == "Coverage":
+            # Get summary using minimal cutoffs.
+            tracks_dataset_type = data_sources['index']['name']
+            converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+            indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset )
+            summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 )
+            if summary == "detail":
+                # Use maximum level of detail--2--to get summary data no matter the resolution.
+                summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 )
+            frequencies, max_v, avg_v, delta = summary
+            return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
+
+        if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
             # Only check for summary_tree if it's Auto mode (which is the default)
             # 
             # Have to choose between indexer and data provider

scripts/migrate_tools/0004_tools.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cd `dirname $0`/../..
+python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@

scripts/migrate_tools/0004_tools.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<toolshed name="toolshed.g2.bx.psu.edu">
+    <repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" />
+    <repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1">
+        <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/>
+        <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/>
+        <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/>
+        <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/>
+        <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/>
+        <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/>
+    </repository>
+</toolshed>

static/scripts/jquery.event.drag.js.patch

@@ -1,10 +0,0 @@
-96c96
-< 			if ( drag.dragging ){
----
-> 			if ( drag.dragging ) {
-99c99,101
-< 				}
----
-> 			} else {
-> 				hijack( event, "dragclickonly", elem );
-> 			}

static/scripts/mvc/history.js

@@ -33,13 +33,13 @@ var HistoryItem = BaseModel.extend({
     
     display     : function(){},
     edit_attr   : function(){},
-    delete      : function(){},
+    remove      : function(){},
     download    : function(){},
     details     : function(){},
     rerun       : function(){},
     tags        : function(){},
     annotations : function(){},
-    peek        : function(){},
+    peek        : function(){}
 });
 
 //..............................................................................
@@ -51,17 +51,17 @@ var HistoryItemView = BaseView.extend({
     icons       : {
         display     : 'path to icon',
         edit_attr   : 'path to icon',
-        delete      : 'path to icon',
+        remove      : 'path to icon',
         download    : 'path to icon',
         details     : 'path to icon',
         rerun       : 'path to icon',
         tags        : 'path to icon',
-        annotations : 'path to icon',
+        annotations : 'path to icon'
     },
     
     render      : function(){
-        this.$el.append( 'div' )
-    },
+        this.$el.append( 'div' );
+    }
     
 });
 
@@ -139,7 +139,7 @@ var HistoryCollectionView = BaseView.extend({
     
     render      : function(){
         
-    },
+    }
     
 });
 

static/scripts/packed/mvc/history.js

@@ -0,0 +1 @@
+var HistoryItem=BaseModel.extend({display:function(){},edit_attr:function(){},remove:function(){},download:function(){},details:function(){},rerun:function(){},tags:function(){},annotations:function(){},peek:function(){}});var HistoryItemView=BaseView.extend({tagName:"div",className:"historyItemContainer",icons:{display:"path to icon",edit_attr:"path to icon",remove:"path to icon",download:"path to icon",details:"path to icon",rerun:"path to icon",tags:"path to icon",annotations:"path to icon"},render:function(){this.$el.append("div")}});var History=Backbone.Collection.extend({});var HistoryCollectionView=BaseView.extend({tagName:"body",className:"historyCollection",render:function(){}});

static/scripts/packed/templates/compiled/panel_section.js

@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<div class="toolSectionTitle" id="title_';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'">\n    <a href="javascript:void(0)"><span>';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+'</span></a>\n</div>\n<div id="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'" class="toolSectionBody" style="display: none; ">\n    <div class="toolSectionBg"></div>\n<div>';return i})})();
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<div class="toolSectionTitle" id="title_';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'">\n    <a href="javascript:void(0)"><span>';g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+'</span></a>\n</div>\n<div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'" class="toolSectionBody" style="display: none; ">\n    <div class="toolSectionBg"></div>\n<div>';return h})})();

static/scripts/packed/templates/compiled/tool_form.js

@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,p,e,n,m){e=e||f.helpers;var k="",c,r,j,i,q=this,g="function",o=e.helperMissing,h=void 0,l=this.escapeExpression;function d(v,u){var s="",t;s+='\n        <div class="form-row">\n            <label for="';j=e.name;t=j||v.name;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"name",{hash:{}})}}s+=l(t)+'">';j=e.label;t=j||v.label;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"label",{hash:{}})}}s+=l(t)+':</label>\n            <div class="form-row-input">\n                ';j=e.html;t=j||v.html;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"html",{hash:{}})}}if(t||t===0){s+=t}s+='\n            </div>\n            <div class="toolParamHelp" style="clear: both;">\n                ';j=e.help;t=j||v.help;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"help",{hash:{}})}}s+=l(t)+'\n            </div>\n            <div style="clear: both;"></div>\n        </div>\n        ';return s}k+='<div class="toolFormTitle">';j=e.name;c=j||p.name;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"name",{hash:{}})}}k+=l(c)+" (version ";j=e.version;c=j||p.version;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"version",{hash:{}})}}k+=l(c)+')</div>\n    <div class="toolFormBody">\n        ';j=e.inputs;c=j||p.inputs;r=e.each;i=q.program(1,d,m);i.hash={};i.fn=i;i.inverse=q.noop;c=r.call(p,c,i);if(c||c===0){k+=c}k+='\n    </div>\n    <div class="form-row form-actions">\n    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n    <div class="toolHelpBody">';j=e.help;c=j||p.help;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"help",{hash:{}})}}k+=l(c)+"</div>\n</div>";return k})})();
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(s,r){var p="",q,o;p+='\n        <div class="form-row">\n            <label for="';o=e.name;if(o){q=o.call(s,{hash:{}})}else{q=s.name;q=typeof q===g?q():q}p+=j(q)+'">';o=e.label;if(o){q=o.call(s,{hash:{}})}else{q=s.label;q=typeof q===g?q():q}p+=j(q)+':</label>\n            <div class="form-row-input">\n                ';o=e.html;if(o){q=o.call(s,{hash:{}})}else{q=s.html;q=typeof q===g?q():q}if(q||q===0){p+=q}p+='\n            </div>\n            <div class="toolParamHelp" style="clear: both;">\n                ';o=e.help;if(o){q=o.call(s,{hash:{}})}else{q=s.help;q=typeof q===g?q():q}p+=j(q)+'\n            </div>\n            <div style="clear: both;"></div>\n        </div>\n        ';return p}i+='<div class="toolFormTitle">';h=e.name;if(h){c=h.call(m,{hash:{}})}else{c=m.name;c=typeof c===g?c():c}i+=j(c)+" (version ";h=e.version;if(h){c=h.call(m,{hash:{}})}else{c=m.version;c=typeof c===g?c():c}i+=j(c)+')</div>\n    <div class="toolFormBody">\n        ';c=m.inputs;c=e.each.call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+='\n    </div>\n    <div class="form-row form-actions">\n    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n    <div class="toolHelpBody">';h=e.help;if(h){c=h.call(m,{hash:{}})}else{c=m.help;c=typeof c===g?c():c}i+=j(c)+"</div>\n</div>";return i})})();

static/scripts/packed/templates/compiled/tool_link.js

@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<a class="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+' tool-link" href="';h=d.link;c=h||n.link;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"link",{hash:{}})}}i+=j(c)+'" target="';h=d.target;c=h||n.target;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"target",{hash:{}})}}i+=j(c)+'" minsizehint="';h=d.min_width;c=h||n.min_width;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"min_width",{hash:{}})}}i+=j(c)+'">';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</a> ";h=d.description;c=h||n.description;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"description",{hash:{}})}}i+=j(c);return i})})();
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<a class="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+' tool-link" href="';g=d.link;if(g){c=g.call(l,{hash:{}})}else{c=l.link;c=typeof c===f?c():c}h+=i(c)+'" target="';g=d.target;if(g){c=g.call(l,{hash:{}})}else{c=l.target;c=typeof c===f?c():c}h+=i(c)+'" minsizehint="';g=d.min_width;if(g){c=g.call(l,{hash:{}})}else{c=l.min_width;c=typeof c===f?c():c}h+=i(c)+'">';g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+"</a> ";g=d.description;if(g){c=g.call(l,{hash:{}})}else{c=l.description;c=typeof c===f?c():c}h+=i(c);return h})})();

static/scripts/packed/templates/compiled/tool_search.js

@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<img src="';h=d.spinner_url;c=h||n.spinner_url;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"spinner_url",{hash:{}})}}i+=j(c)+'" id="search-spinner" class="search-spinner"/>\n';return i})})();
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="icon-button cross-circle tooltip" title="clear search (esc)"> </a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})();

static/scripts/viz/trackster.js

@@ -4433,7 +4433,7 @@ var FeatureTrack = function(view, container, obj_dict) {
     // initialization code.
     //
     var track = this;
-    this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"];
+    this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
     
     //
     // Initialization.
@@ -4516,8 +4516,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var track = this,
             i;
                 
-        // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
-        if (track.mode === "Histogram") {
+        // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
+        if (track.mode === "Coverage") {
             // Get global max.
             var global_max = -1;
             for (i = 0; i < tiles.length; i++) {
@@ -4534,7 +4534,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                     track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
                 }
             }
-        }                
+        }            
         
         //
         // Update filter attributes, UI.
@@ -4649,86 +4649,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
         return slotter.slot_features( features );
     },
-    /**
-     * Given feature data, returns summary tree data. Feature data must be sorted by start 
-     * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
-     * is a two-item list; first item is bin start, second is bin's count.
-     */
-    get_summary_tree_data: function(data, low, high, num_bins) {
-        if (num_bins > high - low) {
-            num_bins = high - low;
-        }
-        var bin_size = Math.floor((high - low)/num_bins),
-            bins = [],
-            max_count = 0;
-            
-        /*    
-        // For debugging:
-        for (var i = 0; i < data.length; i++)
-            console.log("\t", data[i][1], data[i][2], data[i][3]);
-        */
-        
-        //
-        // Loop through bins, counting data for each interval.
-        //
-        var data_index_start = 0,
-            data_index = 0,
-            data_interval,
-            bin_index = 0,
-            bin_interval = [], 
-            cur_bin;
-            
-        // Set bin interval.
-        var set_bin_interval = function(interval, low, bin_index, bin_size) {
-            interval[0] = low + bin_index * bin_size;
-            interval[1] = low + (bin_index + 1) * bin_size;
-        };
-        
-        // Loop through bins, data to compute bin counts. Only compute bin counts as long
-        // as there is data.
-        while (bin_index < num_bins && data_index_start !== data.length) {
-            // Find next bin that has data.
-            var bin_has_data = false;
-            for (; bin_index < num_bins && !bin_has_data; bin_index++) {
-                set_bin_interval(bin_interval, low, bin_index, bin_size);
-                // Loop through data and break if data found that goes in bin.
-                for (data_index = data_index_start; data_index < data.length; data_index++) {
-                    data_interval = data[data_index].slice(1, 3);
-                    if (is_overlap(data_interval, bin_interval)) {
-                        bin_has_data = true;
-                        break;
-                    }
-                }
-                // Break from bin loop if this bin has data.
-                if (bin_has_data) {
-                    break;
-                }
-            }
-            
-            // Set start index to current data, which is the first to overlap with this bin
-            // and perhaps with later bins.
-            data_start_index = data_index;
-            
-            // Count intervals that overlap with bin.
-            bins[bins.length] = cur_bin = [bin_interval[0], 0];
-            for (; data_index < data.length; data_index++) {
-                data_interval = data[data_index].slice(1, 3);
-                if (is_overlap(data_interval, bin_interval)) {
-                    cur_bin[1]++;
-                }
-                else { break; }
-            }
-            
-            // Update max count.
-            if (cur_bin[1] > max_count) {
-                max_count = cur_bin[1];
-            }
-            
-            // Go to next bin.
-            bin_index++;
-        }
-        return {max: max_count, delta: bin_size, data: bins};
-    },
     /**
      * Returns appropriate display mode based on data.
      */
@@ -4766,8 +4686,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * number of pixels required.
      */
     get_canvas_height: function(result, mode, w_scale, canvas_width) {
-        if (mode === "summary_tree" || mode === "Histogram") {
-            // Extra padding at top of summary tree so label does not overlap data.
+        if (mode === "summary_tree" || mode === "Coverage") {
             return this.summary_draw_height;
         }
         else {
@@ -4796,16 +4715,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             tile_high = region.get('end'),
             left_offset = this.left_offset;
         
-        // Drawing the summary tree (feature coverage histogram)
-        if (mode === "summary_tree" || mode === "Histogram") {
-            // Get summary tree data if necessary and set max if there is one.
-            if (result.dataset_type !== "summary_tree") {
-                var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
-                if (result.max) {
-                    st_data.max = result.max;
-                }
-                result = st_data;
-            }
+        // Drawing the summary tree.
+        if (mode === "summary_tree" || mode === "Coverage") {
             // Paint summary tree into canvas
             var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs);
             painter.draw(ctx, canvas.width, canvas.height, w_scale);
@@ -4872,7 +4783,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (mode === "Auto") {
             return true;
         }
-        // All other modes--Histogram, Dense, Squish, Pack--require data + details.
+        // Histogram mode requires summary_tree data.
+        else if (mode === "Coverage") {
+            return data.dataset_type === "summary_tree";
+        }
+        // All other modes--Dense, Squish, Pack--require data + details.
         else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
             return false;
         }

templates/admin/data_admin/data_form.mako

@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako

templates/admin/data_admin/generic_error.mako

@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako

templates/admin/data_admin/local_data.mako

@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako

templates/admin/requests/select_datasets_to_transfer.mako

@@ -8,7 +8,7 @@
    ${common_javascripts()}
 </%def>
 
-${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
+${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
 ${h.css( "dynatree_skin/ui.dynatree" )}
 
 <script type="text/javascript">

templates/admin/tool_shed_repository/browse_repository.mako

@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
 </%def>
 

templates/admin/tool_shed_repository/browse_tool_dependency.mako

@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 

templates/base.mako

@@ -24,9 +24,9 @@
 ## Default javascripts
 <%def name="javascripts()">
   ## <!--[if lt IE 7]>
-  ## <script type='text/javascript' src="/static/scripts/IE7.js"> </script>
+  ## <script type='text/javascript' src="/static/scripts/libs/IE/IE7.js"> </script>
   ## <![endif]-->
-  ${h.js( "jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone", "libs/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
+  ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
   <script type="text/javascript">
       // Set up needed paths.
       var galaxy_paths = new GalaxyPaths({

templates/base_panels.mako

@@ -46,9 +46,9 @@
 ## Default javascripts
 <%def name="javascripts()">
     <!--[if lt IE 7]>
-    ${h.js( 'IE7', 'ie7-recalc' )}
+    ${h.js( 'libs/IE/IE7', 'libs/IE/ie7-recalc' )}
     <![endif]-->
-    ${h.js( 'jquery', 'bootstrap', 'libs/underscore', 'libs/backbone', 'libs/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
+    ${h.js( 'libs/jquery/jquery', 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
     <script type="text/javascript">
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({
@@ -73,7 +73,7 @@
 <%def name="late_javascripts()">
     ## Scripts can be loaded later since they progressively add features to
     ## the panels, but do not change layout
-    ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'jquery.rating', 'galaxy.base', 'galaxy.panels' )}
+    ${h.js( 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.form', 'libs/jquery/jquery.rating', 'galaxy.base', 'galaxy.panels' )}
     <script type="text/javascript">
         
     ensure_dd_helper();

templates/dataset/copy_view.mako

@@ -4,7 +4,7 @@
 <%def name="javascripts()">
 
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
     
     <script type="text/javascript">
         $(function() {

templates/dataset/edit_attributes.mako

@@ -11,7 +11,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${message_ns.javascripts()}
-    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="datatype( dataset, datatypes )">

templates/display_base.mako

@@ -32,9 +32,9 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "bootstrap", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "jquery.rating", 
-            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "jquery.event.drag", "jquery.mousewheel", 
-            "jquery.autocomplete", "jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
+    ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
+            "galaxy.autocom_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
+            "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
         

templates/form.mako

@@ -26,7 +26,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete")}
+    ${h.js("libs/jquery/jquery.autocomplete")}
     <script type="text/javascript">
         $(function(){
             $("input:text:first").focus();

templates/grid_base.mako

@@ -52,7 +52,7 @@
 </%def>
 
 <%def name="grid_javascripts()">
-    ${h.js("jquery.autocomplete", "autocomplete_tagging", "jquery.rating" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )}
     <script type="text/javascript">
         // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are
         // not appended to the identifier of a nested array.