Mercurial > repos > yating-l > hubarchivecreator

changeset 23:1e33b2bd8443 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 17:13:44 -0500
parents 40ded0b51204
children 671d302afbb0
files test-data/bam/__main__.log test-data/bam/bam.html test-data/bam/inputs/HISAT2_Accepted_Hits.bai test-data/bam/inputs/HISAT2_Accepted_Hits.bam test-data/bam/myHub/Dbia3.html test-data/bam/myHub/Dbia3/Dbia3.2bit test-data/bam/myHub/Dbia3/description.html test-data/bam/myHub/Dbia3/groups.txt test-data/bam/myHub/Dbia3/trackDb.txt test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/bam/myHub/genomes.txt test-data/bam/myHub/hub.txt
diffstat 11 files changed, 125 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/__main__.log	Thu Dec 29 17:13:44 2016 -0500
@@ -0,0 +1,20 @@
+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'10', u'name': u'HISAT2_Accepted_Hits', 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: [<Bam.Bam object at 0x17c0b50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/904/dataset_1272_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:----- 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/bam/bam.html	Thu Dec 29 17:13:44 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/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>
+
+                </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/bam/inputs/HISAT2_Accepted_Hits.bai has changed
Binary file test-data/bam/inputs/HISAT2_Accepted_Hits.bam has changed
Binary file test-data/bam/myHub/Dbia3/Dbia3.2bit has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/Dbia3/groups.txt	Thu Dec 29 17:13:44 2016 -0500
@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/Dbia3/trackDb.txt	Thu Dec 29 17:13:44 2016 -0500
@@ -0,0 +1,11 @@
+    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
+
Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed
Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/genomes.txt	Thu Dec 29 17:13:44 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/bam/myHub/hub.txt	Thu Dec 29 17:13:44 2016 -0500
@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html