# HG changeset patch
# User yating-l
# Date 1490813183 14400
# Node ID 193e94a43f0f297455ff8a0c49d2e416a55c294b
# Parent  6803152ea92a6dc7ecef6fd0d92b5ea37554f018
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 88aa9133c8eccdb21dbc755eb9643c9e7b09449e-dirty

diff -r 6803152ea92a -r 193e94a43f0f TrackHub.py
--- a/TrackHub.py	Tue Mar 28 18:13:27 2017 -0400
+++ b/TrackHub.py	Wed Mar 29 14:46:23 2017 -0400
@@ -72,8 +72,20 @@
         print "finished name index \n"
 
     def makeArchive(self):
-        shutil.make_archive(self.out_path, 'zip', self.out_path)  
-        shutil.rmtree(self.out_path) 
+        shutil.make_archive(self.out_path, 'zip', self.out_path)
+        data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'
+        try:
+            if os.path.exists(data_folder):
+                if os.path.isdir(data_folder):
+                    shutil.rmtree(data_folder)
+                else:
+                    os.remove(data_folder)
+        except OSError as oserror:
+            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
+        shutil.copytree(self.out_path, data_folder)
+        p = subprocess.Popen(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
+        p.communicate()
+        shutil.rmtree(self.out_path)
     
     #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
     #run it locally. May need modify
@@ -81,6 +93,7 @@
         with open(self.outfile, 'w') as htmlfile:
             htmlstr = 'The JBrowse Hub is created: <br>'
             zipfiles = '<li><a href = "%s">Download</a></li>'
+            jbrowse_hub = '<li><a href = "http://192.168.56.11/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
             filedir_abs = os.path.abspath(self.outfile)
             filedir = os.path.dirname(filedir_abs)
             filedir = os.path.join(filedir, self.outfolder)
@@ -90,7 +103,7 @@
                         relative_directory = os.path.relpath(root, filedir)
                         relative_file_path = os.path.join(relative_directory, file)
                         htmlstr += zipfiles % relative_file_path
-                        
+            htmlstr += jbrowse_hub
             htmlfile.write(htmlstr)
 
     def createTrackList(self):