2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/f36d687104d6/ Changeset: f36d687104d6 Branch: next-stable User: Dave Bouvier Date: 2013-05-31 18:53:56 Summary: Fix for redundant environment settings in env.sh when set_environment actions are distributed across multiple action sections. Affected #: 1 file

diff -r 835eb008fbabed538d7b10081e05680757646edd -r f36d687104d6c2b0b7e482181a5bf0a24740feb1 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 @@ -431,7 +431,15 @@ else: log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) - actions.append( ( action_type, action_dict ) ) + action_tuple = ( action_type, action_dict ) + # If we're setting environment variables, it's redundant to set the same variable to the same value more than once, + # so we only append it to the actions list if it isn't already there. + if action_type in [ 'set_environment', 'set_environment_for_install' ]: + if action_tuple not in actions: + actions.append( action_tuple ) + # However, there may be cases where other action types should be executed several times with the same parameters. + else: + actions.append( action_tuple ) if actions: actions_dict[ 'actions' ] = actions if proprietary_fabfile_path:

https://bitbucket.org/galaxy/galaxy-central/commits/c37ea459a80b/ Changeset: c37ea459a80b User: Dave Bouvier Date: 2013-05-31 18:54:26 Summary: Merge in next-stable. Affected #: 1 file

diff -r 2e324d02a9633e9b7e0ee5d6535e76afef57d934 -r c37ea459a80b15795f85359536be883ca21fb942 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 @@ -431,7 +431,15 @@ else: log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) - actions.append( ( action_type, action_dict ) ) + action_tuple = ( action_type, action_dict ) + # If we're setting environment variables, it's redundant to set the same variable to the same value more than once, + # so we only append it to the actions list if it isn't already there. + if action_type in [ 'set_environment', 'set_environment_for_install' ]: + if action_tuple not in actions: + actions.append( action_tuple ) + # However, there may be cases where other action types should be executed several times with the same parameters. + else: + actions.append( action_tuple ) if actions: actions_dict[ 'actions' ] = actions if proprietary_fabfile_path:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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