# HG changeset patch # User yating-l # Date 1483114081 18000 # Node ID 875a3346cf90be1f7bdc0ed14cf33a1f60a29003 # Parent d644fd2166f8bc2c34248f919eb30273574dfc58 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/__main__.log --- a/test-data/all_datatypes/__main__.log Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -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: [, , , , , , ] -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! #### diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/all_datatypes_trackhub.html --- a/test-data/all_datatypes/all_datatypes_trackhub.html Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ - - - -

- The following has been generated by Hub Archive Creator: -

- - - - - - diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3.html diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/Dbia3.2bit Binary file test-data/all_datatypes/myHub/Dbia3/Dbia3.2bit has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/description.html diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/groups.txt --- a/test-data/all_datatypes/myHub/Dbia3/groups.txt Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -name default_group -label Default group -priority 2 -defaultIsClosed 0 - diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/trackDb.txt --- a/test-data/all_datatypes/myHub/Dbia3/trackDb.txt Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ - 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 - diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb Binary file test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam Binary file test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai Binary file test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig Binary file test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb Binary file test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb Binary file test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb Binary file test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb Binary file test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb has changed diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/genomes.txt --- a/test-data/all_datatypes/myHub/genomes.txt Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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 diff -r d644fd2166f8 -r 875a3346cf90 test-data/all_datatypes/myHub/hub.txt --- a/test-data/all_datatypes/myHub/hub.txt Fri Dec 30 11:04:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -hub gonrampDbia3 -shortLabel Dbia3 -longLabel Dbia3 -genomesFile genomes.txt -email rmarenco@gwu.edu -descriptionUrl Dbia3.html