{"action":"opened","issue":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/35","repository_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link","labels_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/35/comments","events_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/35/events","html_url":"https://github.com/PacificBiosciences/SMRT-Link/issues/35","id":168094999,"number":35,"title":"Installation with LSF ","user":{"login":"aldonix","id":20703997,"avatar_url":"https://avatars.githubusercontent.com/u/20703997?v=3","gravatar_id":"","url":"https://api.github.com/users/aldonix","html_url":"https://github.com/aldonix","followers_url":"https://api.github.com/users/aldonix/followers","following_url":"https://api.github.com/users/aldonix/following{/other_user}","gists_url":"https://api.github.com/users/aldonix/gists{/gist_id}","starred_url":"https://api.github.com/users/aldonix/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aldonix/subscriptions","organizations_url":"https://api.github.com/users/aldonix/orgs","repos_url":"https://api.github.com/users/aldonix/repos","events_url":"https://api.github.com/users/aldonix/events{/privacy}","received_events_url":"https://api.github.com/users/aldonix/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-07-28T13:26:05Z","updated_at":"2016-07-28T13:26:05Z","closed_at":null,"body":"I believe there is something missing for LSF configuration. Although during installation it properly finds LSF_BINDIR it cannot find the simple command like bsub. running the same command from cli works but if one uses gui or run-sat-services job fails:\r\n>>\r\n$SMRT_ROOT/userdata/jobs_root/000/000005/tasks/pbcoretools.tasks.filterdataset-0/cluster.sh: line 5: bsub: command not found of cmd bash \r\n\r\ndirectory jmsenv in uderdata/generated/config is not created during installation"}}
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