Place the new egg config options into the environment at Galaxy startup since

eggs.require() has no access to the config file.

scripts/paster.py

@@ -7,6 +7,11 @@ top level directly.
 
 import os, sys
 
+try:
+    import configparser
+except:
+    import ConfigParser as configparser
+
 # ensure supported version
 from check_python import check_python
 try:
@@ -19,15 +24,44 @@ new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
 from galaxy import eggs
-import pkg_resources
 
 if 'LOG_TEMPFILES' in os.environ:
     from log_tempfile import TempFile
     _log_tempfile = TempFile()
     import tempfile
 
-pkg_resources.require( "Paste" )
-pkg_resources.require( "PasteDeploy" )
+try:
+    serve = sys.argv.index('serve')
+except:
+    print >>sys.stderr, "Galaxy does not use the real Paste Script, the only supported command is 'serve'"
+    sys.exit(1)
+
+# eggs.require() can be called inside the app without access to the Galaxy
+# config, so we need to push the egg options into the environment so they are
+# available to Crate instantiated in require()
+
+# locate the arg containing the path to the config file
+config = None
+p = configparser.ConfigParser()
+for arg in sys.argv:
+    try:
+        p.read(arg)
+        assert 'app:main' in p.sections()
+        config = arg
+        break
+    except (configparser.Error, AssertionError):
+        pass
+
+# find any egg options set in the config
+crate = eggs.Crate(config)
+for opt in ('enable_eggs', 'enable_egg_fetch', 'try_dependencies_from_env'):
+    env = 'GALAXY_CONFIG_' + opt.upper()
+    # don't overwrite existing env vars configured by the user
+    if env not in os.environ:
+        os.environ[env] = str(getattr(crate.galaxy_config, opt))
+
+eggs.require( "Paste" )
+eggs.require( "PasteDeploy" )
 
 from galaxy.util.pastescript import serve
 serve.run()