Display files from galaxy in IGB (needs copy of synonyms.txt)

igb_bed.xml

<display id="igb_bed" version="1.0.0" name="display in ">
    <link id="igb_bed" name="IGB">
        <url>http://localhost:7085/UnibrowControl?version=${buildversion}&amp;${position}&amp;loadresidues=false&amp;feature_url_0=${bed_file.url}&amp;sym_name_0=${thenicename}&amp;sym_method_0=${bed_file.url}&amp;sym_bg_0=0xFFFFFF&amp;graph_show_label_0=true&amp;graph_show_axis_0=true&amp;graph_minvis_0=0.0&amp;graph_maxvis_0=100&amp;graph_float_0=false&amp;graph_style_0=Bar&amp;query_url=${bed_file.url}&amp;server_url=galaxy</url>
        <param type="data" name="bed_file_for_name" viewable="False"/>
	<param type="template" name="thenicename" viewable="False" strip="True">
#import re
#set nm=$bed_file_for_name.name
${re.sub('\W',"_",nm)}
	</param>
	<param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" />
	<param type="template" name="position" strip="True" >
#set line_count = 0
#set chrom = None
#set start = float( 'inf' )
#set end = 0
#for $line in open( $bed_file.file_name ):
    #if $line_count &gt; 10: ##10 max lines to check for view port
        #break
    #end if
    #if not $line.startswith( "#" ):
        #set $fields = $line.split( "\t" )
        #try:
            #if len( $fields ) &gt;= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ):
                #if $chrom is None or $fields[ $bed_file.metadata.chromCol - 1 ] == $chrom:
                    #set chrom = $fields[ $bed_file.metadata.chromCol - 1 ]
                    #set start = min( $start, int( $fields[ $bed_file.metadata.startCol - 1 ] ) )
                    #set end = max( $end, int( $fields[ $bed_file.metadata.endCol - 1 ] ) )
                #end if
            #end if
        #except:
            #pass
        #end try
    #end if
    #set line_count += 1
#end for
#if $chrom is not None:
seqid=${chrom}&amp;start=${start}&amp;end=${end + 1}
#else:
seqid=chr1&amp;start=10000&amp;end=10100
#end if
        </param>
	<param type="template" name="buildversion" strip="True" >
#set igbkey = "unknown"
#set dbkey=$bed_file.dbkey
#for $line in open('display_applications/igb/synonyms.txt', 'r')
    #set $fields = $line.split( "\t" )
    #for $field in $fields:
         #if $field == dbkey:
            #set igbkey = $fields[0]
            #break
         #end if
    #end for
#end for
${igbkey}
        </param>
    </link>
</display>

Display files from galaxy in IGB

1. create folder igb in display_applications

      mkdir ~/galaxy/display_applications/igb
   

2. copy a synonyms.txt file from the igb distribution there

      cp ~/work/igb/resources/synonyms.txt ~/galaxy/display_applications/igb/synonyms.txt
   

3. copy xml files from this gist there

4. register xml files in datatypes_conf.xml
   for data type bed (search for <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">) and insert

     <display file="igb/igb_bed.xml" />
   

5. restart galaxy and hope for the best

known problems:

there is a problem with the sym_method that has to be created differently. It currenlty prevents the name to be shown in a nice way in the graph (or track - I confuse the two).