# HG changeset patch
# User yating-l
# Date 1490975649 14400
# Node ID 1e4806330e51798fbf4b0418ef15a46d632c812d
# Parent  6fec27968f862b7b0f40a55631f73201d19b67f2
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit a505d6c97db9d044761b5ce92be4a39cb84eda29-dirty

diff -r 6fec27968f86 -r 1e4806330e51 TrackHub.py
--- a/TrackHub.py	Thu Mar 30 18:03:43 2017 -0400
+++ b/TrackHub.py	Fri Mar 31 11:54:09 2017 -0400
@@ -32,8 +32,8 @@
         for input_file in self.input_files:
             self.addTrack(input_file)
         self.indexName()
-        self.makeArchive()
-        self.outHtml()
+        slink = self.makeArchive()
+        self.outHtml(slink)
         print "Success!\n"
     
     def prepareRefseq(self):
@@ -72,7 +72,18 @@
 
     def makeArchive(self):
         shutil.make_archive(self.out_path, 'zip', self.out_path)
-        data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'
+        source = os.path.abspath(self.out_path)
+        slink = source.replace('/', '_')
+        slink = os.path.join('/home/galaxy/galaxy/static/JBrowse-1.12.1/data', slink)
+        try:
+            if os.path.islink(slink):
+                os.unlink(slink)
+        except OSError as oserror:
+            print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
+        os.symlink(source, slink)
+        return slink
+        '''
+        data_folder = '/gonramp/static/JBrowse-1.12.1/jbrowse_hub'
         try:
             if os.path.exists(data_folder):
                 if os.path.isdir(data_folder):
@@ -84,14 +95,15 @@
         shutil.copytree(self.out_path, data_folder)
         subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
         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
-    def outHtml(self):
+    def outHtml(self, slink):
         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 = ":80/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
+            jbrowse_hub = '<li><a href = "/gonramp/static/JBrowse-1.12.1/index.html?data="%s" 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)
@@ -101,7 +113,7 @@
                         relative_directory = os.path.relpath(root, filedir)
                         relative_file_path = os.path.join(relative_directory, file)
                         htmlstr += zipfiles % relative_file_path
-            htmlstr += jbrowse_hub
+            htmlstr += jbrowse_hub % slink
             htmlfile.write(htmlstr)
 
     def createTrackList(self):