# HG changeset patch
# User yating-l
# Date 1483051418 18000
# Node ID 1f2395ac5d83869e641a8c03a19cda2ca22c7b4c
# Parent 896889784581ee34cc706b58a83d9a14c2730459
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
diff -r 896889784581 -r 1f2395ac5d83 test-data/two_groups_no_track/__main__.log
--- a/test-data/two_groups_no_track/__main__.log Thu Dec 29 17:34:37 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_no_track/myHub/Dbia3.html
diff -r 896889784581 -r 1f2395ac5d83 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_no_track/myHub/Dbia3/description.html
diff -r 896889784581 -r 1f2395ac5d83 test-data/two_groups_no_track/myHub/genomes.txt
--- a/test-data/two_groups_no_track/myHub/genomes.txt Thu Dec 29 17:34:37 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_no_track/myHub/hub.txt
--- a/test-data/two_groups_no_track/myHub/hub.txt Thu Dec 29 17:34:37 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 896889784581 -r 1f2395ac5d83 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 17:34:37 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/__main__.log Thu Dec 29 17:43:38 2016 -0500
@@ -0,0 +1,42 @@
+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 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/Dbia3.html
diff -r 896889784581 -r 1f2395ac5d83 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/Dbia3/description.html
diff -r 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt Thu Dec 29 17:43:38 2016 -0500
@@ -0,0 +1,10 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+
+name other_group
+label Other group
+priority 2
+defaultIsClosed 0
+
diff -r 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt Thu Dec 29 17:43:38 2016 -0500
@@ -0,0 +1,22 @@
+ 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 896889784581 -r 1f2395ac5d83 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 896889784581 -r 1f2395ac5d83 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/genomes.txt Thu Dec 29 17:43:38 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 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/hub.txt Thu Dec 29 17:43:38 2016 -0500
@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html
diff -r 896889784581 -r 1f2395ac5d83 test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html Thu Dec 29 17:43:38 2016 -0500
@@ -0,0 +1,73 @@
+
+
+
+
+ The following has been generated by Hub Archive Creator:
+
+
+
+ -
+ myHub
+
+
+ -
+ .
+
+
+
+
+
+
+
+
+