# HG changeset patch
# User yating-l
# Date 1483050677 18000
# Node ID 7c0f5442b53f138ad2abd04b94310b32cd04ea7e
# Parent 6872b9583e26948f48b86eae4de1f36883371530
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/__main__.log
--- a/test-data/two_groups_no_track/__main__.log Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/myHub/Dbia3.html
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit
Binary file test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit has changed
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/myHub/Dbia3/description.html
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/myHub/genomes.txt
--- a/test-data/two_groups_no_track/myHub/genomes.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_no_track/myHub/hub.txt
--- a/test-data/two_groups_no_track/myHub/hub.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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:
-
-
-
- -
- myHub
-
-
- -
- .
-
-
-
-
-
-
-
-
-
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_both/__main__.log
--- a/test-data/two_groups_one_track_both/__main__.log Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_both/myHub/Dbia3.html
diff -r 6872b9583e26 -r 7c0f5442b53f 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_both/myHub/Dbia3/description.html
diff -r 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 6872b9583e26 -r 7c0f5442b53f 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_both/myHub/genomes.txt
--- a/test-data/two_groups_one_track_both/myHub/genomes.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_both/myHub/hub.txt
--- a/test-data/two_groups_one_track_both/myHub/hub.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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:
-
-
-
- -
- myHub
-
-
- -
- .
-
-
-
-
-
-
-
-
-
diff -r 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_first/__main__.log
--- a/test-data/two_groups_one_track_first/__main__.log Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_first/myHub/Dbia3.html
diff -r 6872b9583e26 -r 7c0f5442b53f 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_first/myHub/Dbia3/description.html
diff -r 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_first/myHub/genomes.txt
--- a/test-data/two_groups_one_track_first/myHub/genomes.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f test-data/two_groups_one_track_first/myHub/hub.txt
--- a/test-data/two_groups_one_track_first/myHub/hub.txt Thu Dec 29 17:26:29 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 6872b9583e26 -r 7c0f5442b53f 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 17:26:29 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:
-
-
-
- -
- myHub
-
-
- -
- .
-
-
-
-
-
-
-
-
-