Mercurial > repos > yating-l > hubarchivecreator
changeset 30:1f2395ac5d83 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
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--- 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! ####
--- 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
--- 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
--- 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 @@ - -<html> - <body> - <p> - The following has been generated by Hub Archive Creator: - </p> - <ul> - - <li> - myHub - </li> - <ul> - - <li> - <a href="myHub/Dbia3.html">Dbia3.html</a> - </li> - <li> - <a href="myHub/genomes.txt">genomes.txt</a> - </li> - <li> - <a href="myHub/hub.txt">hub.txt</a> - </li> - <li> - Dbia3 - </li> - <ul> - - <li> - <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> - </li> - <li> - <a href="myHub/Dbia3/description.html">description.html</a> - </li> - - </ul> - - </ul> - <li> - . - </li> - <ul> - - <li> - <a href="./__main__.log">__main__.log</a> - </li> - - </ul> - - </ul> - </body> -</html> - - -
--- /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: [<BigWig.BigWig object at 0x2d26d10>, <Gtf.Gtf object at 0x2d26d50>] +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! ####
--- /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 +
--- /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 +
Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed
Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed
--- /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
--- /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
--- /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 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + +