# HG changeset patch # User rmarenco # Date 1475274783 14400 # Node ID d786bca6a75dcf232557b2111cbb05885a749584 # Parent c02720d1afee66a6a3d53b011e462c54cbc0d149 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3007f4ce1d6e8ac8324970d355f028b9394e2a5f diff -r c02720d1afee -r d786bca6a75d Bam.pyc Binary file Bam.pyc has changed diff -r c02720d1afee -r d786bca6a75d Bed.pyc Binary file Bed.pyc has changed diff -r c02720d1afee -r d786bca6a75d BedSimpleRepeats.pyc Binary file BedSimpleRepeats.pyc has changed diff -r c02720d1afee -r d786bca6a75d BigWig.pyc Binary file BigWig.pyc has changed diff -r c02720d1afee -r d786bca6a75d Datatype.pyc Binary file Datatype.pyc has changed diff -r c02720d1afee -r d786bca6a75d Gff3.pyc Binary file Gff3.pyc has changed diff -r c02720d1afee -r d786bca6a75d Gtf.pyc Binary file Gtf.pyc has changed diff -r c02720d1afee -r d786bca6a75d Psl.pyc Binary file Psl.pyc has changed diff -r c02720d1afee -r d786bca6a75d Track.pyc Binary file Track.pyc has changed diff -r c02720d1afee -r d786bca6a75d TrackDb.pyc Binary file TrackDb.pyc has changed diff -r c02720d1afee -r d786bca6a75d TrackHub.py --- a/TrackHub.py Fri Sep 30 15:14:24 2016 -0400 +++ b/TrackHub.py Fri Sep 30 18:33:03 2016 -0400 @@ -96,6 +96,9 @@ ) trackDbFile.write(htmlMakoRendered) + logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName, + trackDbObject.group_name.lower().replace(' ', '_'))) + def addGroup(self, group_name="Default"): # If not already present in self.groups, add to groups.txt # Create the trackDb.txt file in the specie folder, if not exists @@ -105,6 +108,8 @@ # If the group is already present, we don't need to add it if group_name in self.groups: + logging.debug("We DON'T add in {0} the group {1}".format(groupsTxtFilePath, + group_name)) return # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object @@ -115,6 +120,8 @@ label=group_name ) groupFile.write(htmlMakoRendered) + logging.debug("We just added in {0} the group {1}".format(groupsTxtFilePath, + group_name)) self.groups.add(group_name) def terminate(self): diff -r c02720d1afee -r d786bca6a75d TrackHub.pyc Binary file TrackHub.pyc has changed diff -r c02720d1afee -r d786bca6a75d hubArchiveCreator.py --- a/hubArchiveCreator.py Fri Sep 30 15:14:24 2016 -0400 +++ b/hubArchiveCreator.py Fri Sep 30 18:33:03 2016 -0400 @@ -147,8 +147,13 @@ # Create Ordered Dictionary to add the tracks in the tool form order all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) + logging.debug("----- End of all_datatype_dictionary processing -----") + logging.debug("all_datatype_ordered_dictionary keys are: {0}".format(all_datatype_ordered_dictionary.values())) + + logging.debug("----- Beginning of Track adding processing -----") for index, datatypeObject in all_datatype_ordered_dictionary.iteritems(): trackHub.addTrack(datatypeObject.track.trackDb) + logging.debug("----- End of Track adding processing -----") # We process all the modifications to create the zip file #trackHub.createZip() diff -r c02720d1afee -r d786bca6a75d hubArchiveCreator.xml --- a/hubArchiveCreator.xml Fri Sep 30 15:14:24 2016 -0400 +++ b/hubArchiveCreator.xml Fri Sep 30 18:33:03 2016 -0400 @@ -56,14 +56,32 @@ #silent data_dict.update($extra_data_dict) ## Add the ordering by taking the tool form indexes - #silent $data_dict.update({"order_index": $order_index + 1}) + #silent $data_dict.update({"order_index": $order_index}) #silent $data_parameter_dict.update({$false_path: $data_dict}) #end def + + ## Get the number of digits from tracks, to have a unique integer from group index and track index + + #set temp_max_digit = 0 + + #for $g in $group + #if len($g.format) > $temp_max_digit + #silent temp_max_digit = len($g.format) + #end if + #end for + + #set nb_digits_max_track = len(str($temp_max_digit)) + + ## END Get the number of digits + #for $i_g, $g in enumerate( $group ) #for $i, $f in enumerate( $g.format ) + ## Create the order index using index_group+1 concatenated with index_track + #set index_group_final = str($i_g + 1) + #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) ## For each format, we have a few mandatory fields we store in a dict #set track_color = str($f.formatChoice.track_color) @@ -79,39 +97,39 @@ ## Add Bam format specific fields #silent extra_data_dict.update({"index": $bam_index}) - #silent $prepare_json($f.formatChoice.BAM, $i, extra_data_dict) + #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "bed" #if $f.formatChoice.bedChoice.bed_select == "bed" --bed $f.formatChoice.bedChoice.BED - #silent $prepare_json($f.formatChoice.bedChoice.BED, $i, + #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats - #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i, + #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, extra_data_dict) #end if #end if #if $f.formatChoice.format_select == "psl" --psl $f.formatChoice.PSL - #silent $prepare_json($f.formatChoice.PSL, $i, + #silent $prepare_json($f.formatChoice.PSL, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "bigwig" --bigwig $f.formatChoice.BIGWIG - #silent $prepare_json($f.formatChoice.BIGWIG, $i, + #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "gff3" --gff3 $f.formatChoice.GFF3 - #silent $prepare_json($f.formatChoice.GFF3, $i, + #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "gtf" ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 --gtf $f.formatChoice.GTF - #silent $prepare_json($f.formatChoice.GTF, $i, + #silent $prepare_json($f.formatChoice.GTF, $index_track_final, extra_data_dict) #end if #end for diff -r c02720d1afee -r d786bca6a75d tool_dependencies.xml --- a/tool_dependencies.xml Fri Sep 30 15:14:24 2016 -0400 +++ b/tool_dependencies.xml Fri Sep 30 18:33:03 2016 -0400 @@ -105,27 +105,4 @@ The tools downloaded by this dependency definition are free for academic use. - - - - - - - - http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl - - - http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl - - - - $INSTALL_DIR/bin/pslToBigPsl - - - $INSTALL_DIR/bin - - - - The tools downloaded by this dependency definition are free for academic use. -