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changeset 33:98cc27e63eb4 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
author yating-l
date Thu, 29 Dec 2016 17:54:26 -0500
parents 5e8eae7ddbe8
children 04b942019dce
files test-data/two_groups_multiple_tracks/__main__.log test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html
diffstat 2 files changed, 150 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/__main__.log	Thu Dec 29 17:54:26 2016 -0500
@@ -0,0 +1,68 @@
+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: [<Bam.Bam object at 0x1b78b90>, <BigWig.BigWig object at 0x1b78e10>, <Gtf.Gtf object at 0x1b78e90>, <Gff3.Gff3 object at 0x1b78e50>]
+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! ####
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html	Thu Dec 29 17:54:26 2016 -0500
@@ -0,0 +1,82 @@
+
+<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/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb">Multi-Fasta_GlimmerHMM_Gene_Predictions.bb</a>
+                </li>
+                <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>
+
+
+