2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b766dac9fae/ Changeset: 6b766dac9fae Branch: next-stable User: greg Date: 2013-05-21 22:46:16 Summary: Fix for defining set_environment_for_install tags in multiple tag sets instead of multiple repositories per tag set. Affected #: 2 files diff -r 206050841f67bfc31dfc67773bf815c1506ffe77 -r 6b766dac9faec6e47fca620b514306149954811b lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -131,7 +131,14 @@ tool_dependency_key = '%s/%s' % ( tool_dependency_name, tool_dependency_version ) installation_directory = tool_dependency.installation_directory( app ) env_shell_file_path = get_env_shell_file_path( installation_directory ) - env_shell_file_paths.append( env_shell_file_path ) + if env_shell_file_path: + env_shell_file_paths.append( env_shell_file_path ) + else: + error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency " + error_message += "type %s, name %s, version %s for repository %s" % \ + ( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) ) + log.debug( error_message ) + continue else: error_message = "Skipping tool dependency definition because unable to locate tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ diff -r 206050841f67bfc31dfc67773bf815c1506ffe77 -r 6b766dac9faec6e47fca620b514306149954811b lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -346,6 +346,7 @@ if package_name: actions_dict[ 'package_name' ] = package_name actions = [] + all_env_shell_file_paths = [] for action_elem in actions_elem: action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) @@ -415,7 +416,6 @@ # that above are supported, but in the future other approaches to setting environment variables or other environment attributes can be # supported. The above tag set will result in the installed and compiled numpy version 1.7.1 binary to be used when compiling the current # tool dependency package. See the package_matplotlib_1_2 repository in the test tool shed for a real-world example. - all_env_shell_file_paths = [] for env_elem in action_elem: if env_elem.tag == 'repository': env_shell_file_paths = common_util.get_env_shell_file_paths( app, env_elem ) https://bitbucket.org/galaxy/galaxy-central/commits/f5fe2f094060/ Changeset: f5fe2f094060 User: greg Date: 2013-05-21 22:46:57 Summary: Merged from next-stable Affected #: 2 files diff -r 542f2ba1bc575ab80168280159af642b7caace6f -r f5fe2f0940609a46b6105a2db66da821420f4f99 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -131,7 +131,14 @@ tool_dependency_key = '%s/%s' % ( tool_dependency_name, tool_dependency_version ) installation_directory = tool_dependency.installation_directory( app ) env_shell_file_path = get_env_shell_file_path( installation_directory ) - env_shell_file_paths.append( env_shell_file_path ) + if env_shell_file_path: + env_shell_file_paths.append( env_shell_file_path ) + else: + error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency " + error_message += "type %s, name %s, version %s for repository %s" % \ + ( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) ) + log.debug( error_message ) + continue else: error_message = "Skipping tool dependency definition because unable to locate tool dependency " error_message += "type %s, name %s, version %s for repository %s" % \ diff -r 542f2ba1bc575ab80168280159af642b7caace6f -r f5fe2f0940609a46b6105a2db66da821420f4f99 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -346,6 +346,7 @@ if package_name: actions_dict[ 'package_name' ] = package_name actions = [] + all_env_shell_file_paths = [] for action_elem in actions_elem: action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) @@ -415,7 +416,6 @@ # that above are supported, but in the future other approaches to setting environment variables or other environment attributes can be # supported. The above tag set will result in the installed and compiled numpy version 1.7.1 binary to be used when compiling the current # tool dependency package. See the package_matplotlib_1_2 repository in the test tool shed for a real-world example. - all_env_shell_file_paths = [] for env_elem in action_elem: if env_elem.tag == 'repository': env_shell_file_paths = common_util.get_env_shell_file_paths( app, env_elem ) 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.