changeset 18:a986c9f88d38 draft

removed dependencies

--- a/rgToolFactory.py	Sun Mar 23 07:12:47 2014 -0400
+++ b/rgToolFactory.py	Sun Mar 23 07:28:32 2014 -0400
@@ -8,6 +8,8 @@
 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
 #
 # march 2014
+# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
+# grrrrr - night before a demo
 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
 #
 # added ghostscript and graphicsmagick as dependencies 
@@ -95,10 +97,10 @@
 toolhtmldepskel = """<?xml version="1.0"?>
 <tool_dependency>
     <package name="ghostscript" version="9.10">
-        <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
+        <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
     </package>
     <package name="graphicsmagick" version="1.3.18">
-        <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
+        <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
     </package>
         <readme>
            %s
@@ -362,11 +364,12 @@
                 hlp = open(self.opts.help_text,'r').read()
             else:
                 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
-            tooldepcontent = toolhtmldepskel  % hlp
-            depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
-            depf.write(tooldepcontent)
-            depf.write('\n')
-            depf.close()
+            if self.opts.include_dependencies:
+                tooldepcontent = toolhtmldepskel  % hlp
+                depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
+                depf.write(tooldepcontent)
+                depf.write('\n')
+                depf.close()
         if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
             testdir = os.path.join(tdir,'test-data')
             os.mkdir(testdir) # make tests directory
@@ -653,6 +656,7 @@
     a('--tool_desc',default=None)
     a('--new_tool',default=None)
     a('--tool_version',default=None)
+    a('--include_dependencies',default=None)    
     opts, args = op.parse_args()
     assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
     assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'