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changeset 28:7c0f5442b53f 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 17:31:17 -0500
parents 6872b9583e26
children 896889784581
files test-data/two_groups_no_track/__main__.log test-data/two_groups_no_track/myHub/Dbia3.html test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit test-data/two_groups_no_track/myHub/Dbia3/description.html test-data/two_groups_no_track/myHub/genomes.txt test-data/two_groups_no_track/myHub/hub.txt test-data/two_groups_no_track/two_groups_no_track_trackhub.html test-data/two_groups_one_track_both/__main__.log test-data/two_groups_one_track_both/myHub/Dbia3.html test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit test-data/two_groups_one_track_both/myHub/Dbia3/description.html test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/two_groups_one_track_both/myHub/genomes.txt test-data/two_groups_one_track_both/myHub/hub.txt test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html test-data/two_groups_one_track_first/__main__.log test-data/two_groups_one_track_first/myHub/Dbia3.html test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit test-data/two_groups_one_track_first/myHub/Dbia3/description.html test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig test-data/two_groups_one_track_first/myHub/genomes.txt test-data/two_groups_one_track_first/myHub/hub.txt test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html
diffstat 22 files changed, 0 insertions(+), 371 deletions(-) [+]
line wrap: on
line diff
--- 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! ####
Binary file test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit has changed
--- 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
--- 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
--- 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 @@
-
-<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>
-
-
-
--- 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: [<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! ####
Binary file test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit has changed
--- 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
-
--- 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
-
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
--- 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
--- 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
--- 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 @@
-
-<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>
-
-
-
--- 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: [<BigWig.BigWig object at 0xf57cd0>]
-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! ####
Binary file test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit has changed
--- 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
-
--- 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
-
Binary file test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed
--- 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
--- 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
--- 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 @@
-
-<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/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>
-
-
-