# HG changeset patch # User yating-l # Date 1483111224 18000 # Node ID ed1afba6b16ccfa8855ebf08b1e15e4e6e9a3cfa # Parent 1c7759f382a09d1cec0628598a5ff057108cfda9 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/__main__.log --- a/test-data/two_groups_multiple_tracks/__main__.log Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +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/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat -DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'11', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#000000', u'group_name': u'Default group'} -DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat -DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'} -DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1188.dat -DEBUG:root:data_value: {u'order_index': u'21', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Other 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/svc_galaxy/new/galaxy/database/tmp/tmpC7M6B_.sorted.bigGenePred -DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes -DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb -DEBUG:root:typeOption: bed12+8 -DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as -DEBUG:root:tab option: True -DEBUG:root:Calling bedToBigBed: -DEBUG:root:--------- -DEBUG:root: -DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat -DEBUG:root:data_value: {u'order_index': u'20', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Other 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/svc_galaxy/new/galaxy/database/tmp/tmpirJDCW.sortedBed.bigGenePred -DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes -DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb -DEBUG:root:typeOption: bed12+8 -DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.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/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_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/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_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 just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group -DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group other_group) -DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group -DEBUG:root:We just added track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb (in group other_group) -DEBUG:root:----- End of Track adding processing ----- -DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/myHub/Dbia3.html diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt --- a/test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -name default_group -label Default group -priority 2 -defaultIsClosed 0 - -name other_group -label Other group -priority 2 -defaultIsClosed 0 - diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt --- a/test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - 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 11 - 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 10 - 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 20 - color 0,0,0 - group other_group - - track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb - longLabel Multi-Fasta GlimmerHMM Gene Predictions - shortLabel Multi-Fasta Gli - bigDataUrl tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb - type bigGenePred - visibility dense - thickDrawItem off - priority 21 - color 0,0,0 - group other_group - diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/myHub/genomes.txt --- a/test-data/two_groups_multiple_tracks/myHub/genomes.txt Thu Dec 29 18:24:48 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 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/myHub/hub.txt --- a/test-data/two_groups_multiple_tracks/myHub/hub.txt Thu Dec 29 18:24:48 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 diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html --- a/test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - - -

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

- - - - - - diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/__main__.log --- a/test-data/two_groups_no_track/__main__.log Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +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:----- End of all_datatype_dictionary processing ----- -DEBUG:root:all_datatype_ordered_dictionary keys are: [] -DEBUG:root:----- Beginning of Track adding processing ----- -DEBUG:root:----- End of Track adding processing ----- -DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/myHub/Dbia3.html diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/myHub/Dbia3/description.html diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/myHub/genomes.txt --- a/test-data/two_groups_no_track/myHub/genomes.txt Thu Dec 29 18:24:48 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 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/myHub/hub.txt --- a/test-data/two_groups_no_track/myHub/hub.txt Thu Dec 29 18:24:48 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 diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_no_track/two_groups_no_track_trackhub.html --- a/test-data/two_groups_no_track/two_groups_no_track_trackhub.html Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - - - -

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

- - - - - - diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/__main__.log --- a/test-data/two_groups_one_track_first/__main__.log Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +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/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat -DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'} -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/svc_galaxy/new/galaxy/database/jobs_directory/000/913/dataset_1281_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:----- End of Track adding processing ----- -DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3.html diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit Binary file test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit has changed diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3/description.html diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt --- a/test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt Thu Dec 29 18:24:48 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 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt --- a/test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ - 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 10 - color 0,0,0 - group default_group - diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig Binary file test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/genomes.txt --- a/test-data/two_groups_one_track_first/myHub/genomes.txt Thu Dec 29 18:24:48 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 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/myHub/hub.txt --- a/test-data/two_groups_one_track_first/myHub/hub.txt Thu Dec 29 18:24:48 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 diff -r 1c7759f382a0 -r ed1afba6b16c test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html --- a/test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html Thu Dec 29 18:24:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ - - - -

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

- - - - - -