{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/237","repository_url":"https://api.github.com/repos/CGATOxford/CGATPipelines","labels_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/237/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/237/comments","events_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/237/events","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/237","id":169579460,"number":237,"title":"Add jobs options to cluster options rather than replacing","user":{"login":"IanSudbery","id":5391758,"avatar_url":"https://avatars.githubusercontent.com/u/5391758?v=3","gravatar_id":"","url":"https://api.github.com/users/IanSudbery","html_url":"https://github.com/IanSudbery","followers_url":"https://api.github.com/users/IanSudbery/followers","following_url":"https://api.github.com/users/IanSudbery/following{/other_user}","gists_url":"https://api.github.com/users/IanSudbery/gists{/gist_id}","starred_url":"https://api.github.com/users/IanSudbery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/IanSudbery/subscriptions","organizations_url":"https://api.github.com/users/IanSudbery/orgs","repos_url":"https://api.github.com/users/IanSudbery/repos","events_url":"https://api.github.com/users/IanSudbery/events{/privacy}","received_events_url":"https://api.github.com/users/IanSudbery/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-08-05T10:35:35Z","updated_at":"2016-08-22T10:20:55Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/pulls/237","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/237","diff_url":"https://github.com/CGATOxford/CGATPipelines/pull/237.diff","patch_url":"https://github.com/CGATOxford/CGATPipelines/pull/237.patch"},"body":"Previously P.run chceked if job options were set, and if they are, overwrites cluster_options with them. \r\nThis brakes the ability to set cluster_options in the `.cgat` file. This PR changes the logic so that local job_options are added to cluster_options rather than overwritting them.\r\n\r\n**As this PR changes existing logic i'd appreciate a second opinion on the suitability.** "},"comment":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/comments/241371658","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/237#issuecomment-241371658","issue_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/237","id":241371658,"user":{"login":"AndreasHeger","id":4426336,"avatar_url":"https://avatars.githubusercontent.com/u/4426336?v=3","gravatar_id":"","url":"https://api.github.com/users/AndreasHeger","html_url":"https://github.com/AndreasHeger","followers_url":"https://api.github.com/users/AndreasHeger/followers","following_url":"https://api.github.com/users/AndreasHeger/following{/other_user}","gists_url":"https://api.github.com/users/AndreasHeger/gists{/gist_id}","starred_url":"https://api.github.com/users/AndreasHeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AndreasHeger/subscriptions","organizations_url":"https://api.github.com/users/AndreasHeger/orgs","repos_url":"https://api.github.com/users/AndreasHeger/repos","events_url":"https://api.github.com/users/AndreasHeger/events{/privacy}","received_events_url":"https://api.github.com/users/AndreasHeger/received_events","type":"User","site_admin":false},"created_at":"2016-08-22T10:20:55Z","updated_at":"2016-08-22T10:20:55Z","body":"Thanks, both. I don't know how libdrmaa deals with duplicate options, but I think it is good to keep overwrite semantics in some form. For example, if you try to set cluster options from the command line you expect the original ones to be ignored.\r\n\r\nMaybe fixing the .cgat file is a separate issue."}}
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