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changeset 44:875a3346cf90 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
author yating-l
date Fri, 30 Dec 2016 11:08:01 -0500
parents d644fd2166f8
children 2219ff196405
files test-data/all_datatypes/__main__.log test-data/all_datatypes/all_datatypes_trackhub.html test-data/all_datatypes/myHub/Dbia3.html test-data/all_datatypes/myHub/Dbia3/Dbia3.2bit test-data/all_datatypes/myHub/Dbia3/description.html test-data/all_datatypes/myHub/Dbia3/groups.txt test-data/all_datatypes/myHub/Dbia3/trackDb.txt test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb test-data/all_datatypes/myHub/genomes.txt test-data/all_datatypes/myHub/hub.txt
diffstat 15 files changed, 0 insertions(+), 309 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/all_datatypes/__main__.log	Fri Dec 30 11:04:35 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +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/galaxy/Dev/galaxy/database/files/002/dataset_2738.dat
-DEBUG:root:data_value: {u'index': u'/home/galaxy/Dev/galaxy/database/files/_metadata_files/000/metadata_61.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits.bam', u'track_color': u'#000000', u'group_name': u'Default group'}
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2739.dat
-DEBUG:root:data_value: {u'order_index': u'11', u'name': u'TBLASTN_Alignment_to_proteins', u'track_color': u'#000000', u'group_name': u'Default group'}
-DEBUG:root:Calling sort:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpgvTufo.sortedBed
-DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
-DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb
-DEBUG:root:typeOption: None
-DEBUG:root:autoSql: None
-DEBUG:root:tab option: False
-DEBUG:root:Calling bedToBigBed:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2742.dat
-DEBUG:root:data_value: {u'order_index': u'14', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2740.dat
-DEBUG:root:data_value: {u'order_index': u'12', u'name': u'Repeating_Elements_by_TrfBig', u'track_color': u'#000000', u'group_name': u'Default group'}
-DEBUG:root:Calling sort:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpn63XX6.sortedBed
-DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
-DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb
-DEBUG:root:typeOption: bed4+12
-DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/trf_simpleRepeat.as
-DEBUG:root:tab option: False
-DEBUG:root:Calling bedToBigBed:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2743.dat
-DEBUG:root:data_value: {u'order_index': u'15', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default 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/galaxy/Dev/galaxy/database/tmp/tmp6noWC0.sorted.bigGenePred
-DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
-DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb
-DEBUG:root:typeOption: bed12+8
-DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as
-DEBUG:root:tab option: True
-DEBUG:root:Calling bedToBigBed:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2744.dat
-DEBUG:root:data_value: {u'order_index': u'16', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default 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/galaxy/Dev/galaxy/database/tmp/tmp9EgTcK.sortedBed.bigGenePred
-DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
-DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
-DEBUG:root:typeOption: bed12+8
-DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as
-DEBUG:root:tab option: True
-DEBUG:root:Calling bedToBigBed:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2741.dat
-DEBUG:root:data_value: {u'order_index': u'13', u'name': u'blastXmlToPsl', u'track_color': u'#000000', u'group_name': u'Default group'}
-DEBUG:root:Calling pslToBigPsl:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:Calling sort:
-DEBUG:root:---------
-DEBUG:root:	
-DEBUG:root:Hello
-DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpB6cFUgpsl
-DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
-DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/blastXmlToPsl.bb
-DEBUG:root:typeOption: bed12+12
-DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigPsl.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: [<Bed.Bed object at 0x7f91d06b5fd0>, <Bam.Bam object at 0x7f91d06b5e50>, <Psl.Psl object at 0x7f91d06b5910>, <BedSimpleRepeats.BedSimpleRepeats object at 0x7f91d06b5b10>, <Gff3.Gff3 object at 0x7f91d06b5c90>, <BigWig.BigWig object at 0x7f91d06b5990>, <Gtf.Gtf object at 0x7f91d06b57d0>]
-DEBUG:root:----- Beginning of Track adding processing -----
-DEBUG:root:We just added in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
-DEBUG:root:We just added track TBLASTN_Alignment_to_proteins.bb (in group default_group)
-DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_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/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
-DEBUG:root:We just added track blastXmlToPsl.bb (in group default_group)
-DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
-DEBUG:root:We just added track Repeating_Elements_by_TrfBig.bb (in group default_group)
-DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
-DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group)
-DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_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 DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
-DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
-DEBUG:root:----- End of Track adding processing -----
-DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####
--- a/test-data/all_datatypes/all_datatypes_trackhub.html	Fri Dec 30 11:04:35 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +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/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/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</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>
-
-
-
Binary file test-data/all_datatypes/myHub/Dbia3/Dbia3.2bit has changed
--- a/test-data/all_datatypes/myHub/Dbia3/groups.txt	Fri Dec 30 11:04:35 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
-
--- a/test-data/all_datatypes/myHub/Dbia3/trackDb.txt	Fri Dec 30 11:04:35 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-    track TBLASTN_Alignment_to_proteins.bb
-    longLabel TBLASTN Alignment to proteins
-    shortLabel TBLASTN Alignme
-    bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb
-    type bigBed
-    visibility dense
-    thickDrawItem off
-    priority 11
-    color 0,0,0
-    group default_group
-
-    track HISAT2_Accepted_Hits.bam
-    longLabel HISAT2 Accepted Hits.bam
-    shortLabel HISAT2 Accepted
-    bigDataUrl tracks/HISAT2_Accepted_Hits.bam
-    type bam
-    visibility pack
-    thickDrawItem off
-    priority 10
-    color 0,0,0
-    group default_group
-
-    track blastXmlToPsl.bb
-    longLabel blastXmlToPsl
-    shortLabel blastXmlToPsl
-    bigDataUrl tracks/blastXmlToPsl.bb
-    type bigPsl
-    visibility dense
-    thickDrawItem off
-    priority 13
-    color 0,0,0
-    group default_group
-
-    track Repeating_Elements_by_TrfBig.bb
-    longLabel Repeating Elements by TrfBig
-    shortLabel Repeating Eleme
-    bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb
-    type bigBed 4 +
-    visibility dense
-    thickDrawItem off
-    priority 12
-    color 0,0,0
-    group default_group
-
-    track Augustus_Gene_Predictions.bb
-    longLabel Augustus Gene Predictions
-    shortLabel Augustus Gene P
-    bigDataUrl tracks/Augustus_Gene_Predictions.bb
-    type bigGenePred
-    visibility dense
-    thickDrawItem off
-    priority 15
-    color 0,0,0
-    group default_group
-
-    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 14
-    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 16
-    color 0,0,0
-    group default_group
-
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb has changed
Binary file test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb has changed
--- a/test-data/all_datatypes/myHub/genomes.txt	Fri Dec 30 11:04:35 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/all_datatypes/myHub/hub.txt	Fri Dec 30 11:04:35 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