# HG changeset patch # User yating-l # Date 1483051612 18000 # Node ID 4f903a869fe4050c6a9fe75084d3676cfa8fc872 # Parent 1f2395ac5d83869e641a8c03a19cda2ca22c7b4c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/__main__.log --- a/test-data/two_groups_one_track_both/__main__.log Thu Dec 29 17:43:38 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +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: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/tmpqNltxC.sortedBed.bigGenePred -DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmplv6Lna.chrom.sizes -DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/914/dataset_1282_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/000/914/dataset_1282_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/000/914/dataset_1282_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:----- End of Track adding processing ----- -DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3.html diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit Binary file test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit has changed diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/description.html diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt --- a/test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt Thu Dec 29 17:43:38 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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt --- a/test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt Thu Dec 29 17:43:38 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +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 - - 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 - diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/genomes.txt --- a/test-data/two_groups_one_track_both/myHub/genomes.txt Thu Dec 29 17:43:38 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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/myHub/hub.txt --- a/test-data/two_groups_one_track_both/myHub/hub.txt Thu Dec 29 17:43:38 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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html --- a/test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html Thu Dec 29 17:43:38 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ - - - -

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

- - - - - - diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/__main__.log Thu Dec 29 17:46:52 2016 -0500 @@ -0,0 +1,20 @@ +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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/Dbia3.html diff -r 1f2395ac5d83 -r 4f903a869fe4 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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/Dbia3/description.html diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt Thu Dec 29 17:46:52 2016 -0500 @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt Thu Dec 29 17:46:52 2016 -0500 @@ -0,0 +1,11 @@ + 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 1f2395ac5d83 -r 4f903a869fe4 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 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/genomes.txt Thu Dec 29 17:46:52 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 diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/hub.txt Thu Dec 29 17:46:52 2016 -0500 @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email rmarenco@gwu.edu +descriptionUrl Dbia3.html diff -r 1f2395ac5d83 -r 4f903a869fe4 test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html Thu Dec 29 17:46:52 2016 -0500 @@ -0,0 +1,70 @@ + + + +

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

+ + + + + +