{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/169","labels_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/169/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/169/comments","events_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/169/events","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/169","id":130439072,"number":169,"title":"SLURM","user":{"login":"snsansom","id":4218768,"avatar_url":"https://avatars.githubusercontent.com/u/4218768?v=3","gravatar_id":"","url":"https://api.github.com/users/snsansom","html_url":"https://github.com/snsansom","followers_url":"https://api.github.com/users/snsansom/followers","following_url":"https://api.github.com/users/snsansom/following{/other_user}","gists_url":"https://api.github.com/users/snsansom/gists{/gist_id}","starred_url":"https://api.github.com/users/snsansom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/snsansom/subscriptions","organizations_url":"https://api.github.com/users/snsansom/orgs","repos_url":"https://api.github.com/users/snsansom/repos","events_url":"https://api.github.com/users/snsansom/events{/privacy}","received_events_url":"https://api.github.com/users/snsansom/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-01T18:13:30Z","updated_at":"2016-02-01T18:29:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/pulls/169","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/169","diff_url":"https://github.com/CGATOxford/CGATPipelines/pull/169.diff","patch_url":"https://github.com/CGATOxford/CGATPipelines/pull/169.patch"},"body":"Andreas/Sebastian please take a look!\r\n\r\nThis: \r\n\r\n(1) adds support for the SLURM queue manager assuming that it is configured with consumable resources as commented in the code (a standard configuration profile).\r\n\r\nWe are using SLURM on our cluster so this should get extensive testing.\r\n\r\n(2) implements site-wide configuration in /etc/cgat/. Here /etc/cgat/pipeline.ini is used for pipeline configuration, analogously /etc/cgat/scripts.ini could be used for the CGAT scripts collection.\r\n\r\nThis is needed to allow straightforward (i.e. administrator rather than user configured)  deployment of the code on foreign clusters.\r\n"},"comment":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/comments/178112428","html_url":"https://github.com/CGATOxford/CGATPipelines/pull/169#issuecomment-178112428","issue_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/169","id":178112428,"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},"created_at":"2016-02-01T18:29:54Z","updated_at":"2016-02-01T18:29:54Z","body":"Hi Steve,\r\n\r\nJust a note to say that the '-V' option passed to SGE signifies that the current environment (i.e. the state of environment variables in the current login session) should be passed to the session on the worker node. This ensures that things like the current working dir and the contents of PATH are the same on the head node and the worker node. \r\n\r\nI don't know if this would be necessary for SLURM. "}}