Mercurial > repos > yating-l > hubarchivecreator
changeset 24:671d302afbb0 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/__main__.log Thu Dec 29 17:16:08 2016 -0500 @@ -0,0 +1,120 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2738.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/Dev/galaxy/database/files/_metadata_files/000/metadata_61.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits.bam', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2739.dat +DEBUG:root:data_value: {u'order_index': u'11', u'name': u'TBLASTN_Alignment_to_proteins', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpgvTufo.sortedBed +DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb +DEBUG:root:typeOption: None +DEBUG:root:autoSql: None +DEBUG:root:tab option: False +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2742.dat +DEBUG:root:data_value: {u'order_index': u'14', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2740.dat +DEBUG:root:data_value: {u'order_index': u'12', u'name': u'Repeating_Elements_by_TrfBig', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpn63XX6.sortedBed +DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb +DEBUG:root:typeOption: bed4+12 +DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/trf_simpleRepeat.as +DEBUG:root:tab option: False +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2743.dat +DEBUG:root:data_value: {u'order_index': u'15', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gff3ToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp6noWC0.sorted.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2744.dat +DEBUG:root:data_value: {u'order_index': u'16', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp9EgTcK.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2741.dat +DEBUG:root:data_value: {u'order_index': u'13', u'name': u'blastXmlToPsl', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling pslToBigPsl: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Hello +DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpB6cFUgpsl +DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/blastXmlToPsl.bb +DEBUG:root:typeOption: bed12+12 +DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigPsl.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bed.Bed object at 0x7f91d06b5fd0>, <Bam.Bam object at 0x7f91d06b5e50>, <Psl.Psl object at 0x7f91d06b5910>, <BedSimpleRepeats.BedSimpleRepeats object at 0x7f91d06b5b10>, <Gff3.Gff3 object at 0x7f91d06b5c90>, <BigWig.BigWig object at 0x7f91d06b5990>, <Gtf.Gtf object at 0x7f91d06b57d0>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track TBLASTN_Alignment_to_proteins.bb (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track blastXmlToPsl.bb (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track Repeating_Elements_by_TrfBig.bb (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/all_datatypes_trackhub.html Thu Dec 29 17:16:08 2016 -0500 @@ -0,0 +1,91 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/Dbia3/groups.txt Thu Dec 29 17:16:08 2016 -0500 @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/Dbia3/trackDb.txt Thu Dec 29 17:16:08 2016 -0500 @@ -0,0 +1,77 @@ + track TBLASTN_Alignment_to_proteins.bb + longLabel TBLASTN Alignment to proteins + shortLabel TBLASTN Alignme + bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb + type bigBed + visibility dense + thickDrawItem off + priority 11 + color 0,0,0 + group default_group + + track HISAT2_Accepted_Hits.bam + longLabel HISAT2 Accepted Hits.bam + shortLabel HISAT2 Accepted + bigDataUrl tracks/HISAT2_Accepted_Hits.bam + type bam + visibility pack + thickDrawItem off + priority 10 + color 0,0,0 + group default_group + + track blastXmlToPsl.bb + longLabel blastXmlToPsl + shortLabel blastXmlToPsl + bigDataUrl tracks/blastXmlToPsl.bb + type bigPsl + visibility dense + thickDrawItem off + priority 13 + color 0,0,0 + group default_group + + track Repeating_Elements_by_TrfBig.bb + longLabel Repeating Elements by TrfBig + shortLabel Repeating Eleme + bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb + type bigBed 4 + + visibility dense + thickDrawItem off + priority 12 + color 0,0,0 + group default_group + + track Augustus_Gene_Predictions.bb + longLabel Augustus Gene Predictions + shortLabel Augustus Gene P + bigDataUrl tracks/Augustus_Gene_Predictions.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 15 + color 0,0,0 + group default_group + + track RNA-Seq_Alignment_Summary.bigwig + longLabel RNA-Seq Alignment Summary + shortLabel RNA-Seq Alignme + bigDataUrl tracks/RNA-Seq_Alignment_Summary.bigwig + type bigWig + visibility full + thickDrawItem off + priority 14 + color 0,0,0 + group default_group + + track StringTie_Assembled_Transcripts.bb + longLabel StringTie Assembled Transcripts + shortLabel StringTie Assem + bigDataUrl tracks/StringTie_Assembled_Transcripts.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 16 + color 0,0,0 + group default_group +
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/genomes.txt Thu Dec 29 17:16:08 2016 -0500 @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html