1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/203623b93150/ Changeset: 203623b93150 User: greg Date: 2014-04-24 21:11:43 Summary: Fix for the execute_step() method in the SetEnvironment class. Affected #: 1 file diff -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 -r 203623b931507dcd182e2521911ab036021faf61 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -450,14 +450,20 @@ env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = self.handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) + env_var_dict = self.handle_environment_variables( app=app, + install_environment=install_environment, + tool_dependency=tool_dependency, + install_dir=install_dir, + env_var_dict=env_var_dict, + set_prior_environment_commands=cmds ) env_file_builder.append_line( **env_var_dict ) # The caller should check the status of the returned tool_dependency since return_code is not # returned by this function. return_code = env_file_builder.return_code return tool_dependency, None, None - def handle_environment_variables( self, app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): + def handle_environment_variables( self, app, install_environment, tool_dependency, install_dir, env_var_dict, + set_prior_environment_commands ): """ This method works with with a combination of three tool dependency definition tag sets, which are defined in the tool_dependencies.xml file in the order discussed here. The example for this discussion is the @@ -539,7 +545,6 @@ set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - install_environment = recipe_manager.InstallEnvironment() command_return = install_environment.handle_command( app, tool_dependency, install_dir, command, return_output=True ) # And extract anything labeled with the name of the environment variable we're populating here. if '%s: ' % inherited_env_var_name in command_return: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.