{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/850","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/850/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/850/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/850/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/850","id":75885123,"number":850,"title":"GATK java version issues","user":{"login":"matthdsm","id":11850640,"avatar_url":"https://avatars.githubusercontent.com/u/11850640?v=3","gravatar_id":"","url":"https://api.github.com/users/matthdsm","html_url":"https://github.com/matthdsm","followers_url":"https://api.github.com/users/matthdsm/followers","following_url":"https://api.github.com/users/matthdsm/following{/other_user}","gists_url":"https://api.github.com/users/matthdsm/gists{/gist_id}","starred_url":"https://api.github.com/users/matthdsm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthdsm/subscriptions","organizations_url":"https://api.github.com/users/matthdsm/orgs","repos_url":"https://api.github.com/users/matthdsm/repos","events_url":"https://api.github.com/users/matthdsm/events{/privacy}","received_events_url":"https://api.github.com/users/matthdsm/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-13T07:40:32Z","updated_at":"2015-05-22T12:17:11Z","closed_at":"2015-05-22T12:17:11Z","body":"Hi Brad,\r\n\r\nI finally succeeded get a working installation of bcbio, but now I ran into another problem. I'd like to use our cluster system to perform the analysis (using iPython), but keep running into java issues. Our nodes run on a Ubuntu 12 LTS system with a torque resource manager. The default system java is 1.6, but we also have 1.7 installed. I modified $PATH and $JAVA_HOME in my personal environment en the environment of the node to point to the java 1.7 version, but I keep getting errors when starting GATK because bcbio only seems to detect the 1.6 version in usr/bin.\r\nWhen I try to run an analysis locally everything works flawless and I get no errors.\r\n\r\nAny suggestions? Is there any way I can configure bcbio/iPython to use java 1.7?\r\n\r\n\r\nThanks!\r\nMatthias"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/104646535","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/850#issuecomment-104646535","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/850","id":104646535,"user":{"login":"matthdsm","id":11850640,"avatar_url":"https://avatars.githubusercontent.com/u/11850640?v=3","gravatar_id":"","url":"https://api.github.com/users/matthdsm","html_url":"https://github.com/matthdsm","followers_url":"https://api.github.com/users/matthdsm/followers","following_url":"https://api.github.com/users/matthdsm/following{/other_user}","gists_url":"https://api.github.com/users/matthdsm/gists{/gist_id}","starred_url":"https://api.github.com/users/matthdsm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthdsm/subscriptions","organizations_url":"https://api.github.com/users/matthdsm/orgs","repos_url":"https://api.github.com/users/matthdsm/repos","events_url":"https://api.github.com/users/matthdsm/events{/privacy}","received_events_url":"https://api.github.com/users/matthdsm/received_events","type":"User","site_admin":false},"created_at":"2015-05-22T12:17:11Z","updated_at":"2015-05-22T12:17:11Z","body":"Hi Brad,\r\n\r\nTurns out this was a non issue, we edited the path, but forgot to restart the  torque engine. Sorry to waste your time!\r\n\r\nMatthias "}}