{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/211","labels_url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/211/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/211/comments","events_url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/211/events","html_url":"https://github.com/chapmanb/cloudbiolinux/pull/211","id":120500338,"number":211,"title":"Use sudo when installing gemini","user":{"login":"rchekaluk","id":239735,"avatar_url":"https://avatars.githubusercontent.com/u/239735?v=3","gravatar_id":"","url":"https://api.github.com/users/rchekaluk","html_url":"https://github.com/rchekaluk","followers_url":"https://api.github.com/users/rchekaluk/followers","following_url":"https://api.github.com/users/rchekaluk/following{/other_user}","gists_url":"https://api.github.com/users/rchekaluk/gists{/gist_id}","starred_url":"https://api.github.com/users/rchekaluk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rchekaluk/subscriptions","organizations_url":"https://api.github.com/users/rchekaluk/orgs","repos_url":"https://api.github.com/users/rchekaluk/repos","events_url":"https://api.github.com/users/rchekaluk/events{/privacy}","received_events_url":"https://api.github.com/users/rchekaluk/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-12-04T22:34:20Z","updated_at":"2015-12-05T15:23:04Z","closed_at":"2015-12-05T15:16:09Z","pull_request":{"url":"https://api.github.com/repos/chapmanb/cloudbiolinux/pulls/211","html_url":"https://github.com/chapmanb/cloudbiolinux/pull/211","diff_url":"https://github.com/chapmanb/cloudbiolinux/pull/211.diff","patch_url":"https://github.com/chapmanb/cloudbiolinux/pull/211.patch"},"body":"Use sudo when installing gemini; on Ubuntu this installs to /usr/local and /usr/local/share/gemini.\r\n\r\nRelated to https://github.com/arq5x/gemini/issues/603\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/comments/162212092","html_url":"https://github.com/chapmanb/cloudbiolinux/pull/211#issuecomment-162212092","issue_url":"https://api.github.com/repos/chapmanb/cloudbiolinux/issues/211","id":162212092,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2015-12-05T15:23:04Z","updated_at":"2015-12-05T15:23:04Z","body":"Thanks much for the patch and sorry about the problems. The custom packages in CloudBioLinux are slowly being phased out in favor of proper package management with conda. The GEMINI install script here was out of date and used the options in the previous GEMINI installer which has sudo built into it. To avoid confusion, I removed the out of data custom gemini install and will also plan to remove/deprecate the other custom functions over time.\r\n\r\nIf you'd like to install GEMINI I recommend using the GEMINI installer directly or for a more complete set of packages use the integration with bcbio:\r\n\r\nhttps://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#gemini\r\n\r\nThanks again and hope this helps.\r\n\r\nhttps://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#gemini"}}