Merge pull request galaxyproject#195 from natefoo/fix_galaxy_lib_dir

[STABLE] Ensure JobWrapper.galaxy_lib_dir is set

lib/galaxy/jobs/__init__.py

@@ -720,7 +720,7 @@ def __init__( self, job, queue, use_persisted_destination=False ):
         # Tool versioning variables
         self.write_version_cmd = None
         self.version_string = ""
-        self.galaxy_lib_dir = None
+        self.__galaxy_lib_dir = None
         # With job outputs in the working directory, we need the working
         # directory to be set before prepare is run, or else premature deletion
         # and job recovery fail.
@@ -769,6 +769,12 @@ def get_parallelism(self):
     def commands_in_new_shell(self):
         return self.app.config.commands_in_new_shell
 
+    @property
+    def galaxy_lib_dir(self):
+        if self.__galaxy_lib_dir is None:
+            self.__galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
+        return self.__galaxy_lib_dir
+
     # legacy naming
     get_job_runner = get_job_runner_url
 
@@ -830,8 +836,8 @@ def get_special( ):
         self.sa_session.flush()
 
         self.command_line, self.extra_filenames = tool_evaluator.build()
-        # FIXME: for now, tools get Galaxy's lib dir in their path
-        self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
+        # Ensure galaxy_lib_dir is set in case there are any later chdirs
+        self.galaxy_lib_dir
         # Shell fragment to inject dependencies
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands()
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
@@ -1631,9 +1637,8 @@ def prepare( self, compute_environment=None ):
 
         self.command_line, self.extra_filenames = tool_evaluator.build()
 
-        # FIXME: for now, tools get Galaxy's lib dir in their path
-        if self.command_line and self.command_line.startswith( 'python' ):
-            self.galaxy_lib_dir = os.path.abspath( "lib" )  # cwd = galaxy root
+        # Ensure galaxy_lib_dir is set in case there are any later chdirs
+        self.galaxy_lib_dir
         # Shell fragment to inject dependencies
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands()
         # We need command_line persisted to the db in order for Galaxy to re-queue the job