{"action":"created","issue":{"url":"https://api.github.com/repos/twestbrookunh/paladin/issues/3","labels_url":"https://api.github.com/repos/twestbrookunh/paladin/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/twestbrookunh/paladin/issues/3/comments","events_url":"https://api.github.com/repos/twestbrookunh/paladin/issues/3/events","html_url":"https://github.com/twestbrookunh/paladin/issues/3","id":96567414,"number":3,"title":"paladin prep?","user":{"login":"macmanes","id":164752,"avatar_url":"https://avatars.githubusercontent.com/u/164752?v=3","gravatar_id":"","url":"https://api.github.com/users/macmanes","html_url":"https://github.com/macmanes","followers_url":"https://api.github.com/users/macmanes/followers","following_url":"https://api.github.com/users/macmanes/following{/other_user}","gists_url":"https://api.github.com/users/macmanes/gists{/gist_id}","starred_url":"https://api.github.com/users/macmanes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macmanes/subscriptions","organizations_url":"https://api.github.com/users/macmanes/orgs","repos_url":"https://api.github.com/users/macmanes/repos","events_url":"https://api.github.com/users/macmanes/events{/privacy}","received_events_url":"https://api.github.com/users/macmanes/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/twestbrookunh/paladin/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/twestbrookunh/paladin/milestones/1","html_url":"https://github.com/twestbrookunh/paladin/milestones/version%201.0.0","labels_url":"https://api.github.com/repos/twestbrookunh/paladin/milestones/1/labels","id":1221899,"number":1,"title":"version 1.0.0","description":"","creator":{"login":"macmanes","id":164752,"avatar_url":"https://avatars.githubusercontent.com/u/164752?v=3","gravatar_id":"","url":"https://api.github.com/users/macmanes","html_url":"https://github.com/macmanes","followers_url":"https://api.github.com/users/macmanes/followers","following_url":"https://api.github.com/users/macmanes/following{/other_user}","gists_url":"https://api.github.com/users/macmanes/gists{/gist_id}","starred_url":"https://api.github.com/users/macmanes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macmanes/subscriptions","organizations_url":"https://api.github.com/users/macmanes/orgs","repos_url":"https://api.github.com/users/macmanes/repos","events_url":"https://api.github.com/users/macmanes/events{/privacy}","received_events_url":"https://api.github.com/users/macmanes/received_events","type":"User","site_admin":false},"open_issues":0,"closed_issues":4,"state":"open","created_at":"2015-07-23T11:20:13Z","updated_at":"2015-11-25T05:07:33Z","due_on":null,"closed_at":null},"comments":6,"created_at":"2015-07-22T13:25:56Z","updated_at":"2015-11-25T05:07:33Z","closed_at":"2015-11-25T05:07:33Z","body":"Should we make a `paladin prep` that downloads the reference and indexes it automatically. Most people will use Uniprot. Could be `paladin prep --reference uniprot`.\r\n\r\nCould be `prep`, `setup`, `prepare`, `download`, or something like that.. "},"comment":{"url":"https://api.github.com/repos/twestbrookunh/paladin/issues/comments/159493475","html_url":"https://github.com/twestbrookunh/paladin/issues/3#issuecomment-159493475","issue_url":"https://api.github.com/repos/twestbrookunh/paladin/issues/3","id":159493475,"user":{"login":"twestbrookunh","id":11213717,"avatar_url":"https://avatars.githubusercontent.com/u/11213717?v=3","gravatar_id":"","url":"https://api.github.com/users/twestbrookunh","html_url":"https://github.com/twestbrookunh","followers_url":"https://api.github.com/users/twestbrookunh/followers","following_url":"https://api.github.com/users/twestbrookunh/following{/other_user}","gists_url":"https://api.github.com/users/twestbrookunh/gists{/gist_id}","starred_url":"https://api.github.com/users/twestbrookunh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/twestbrookunh/subscriptions","organizations_url":"https://api.github.com/users/twestbrookunh/orgs","repos_url":"https://api.github.com/users/twestbrookunh/repos","events_url":"https://api.github.com/users/twestbrookunh/events{/privacy}","received_events_url":"https://api.github.com/users/twestbrookunh/received_events","type":"User","site_admin":false},"created_at":"2015-11-25T05:07:33Z","updated_at":"2015-11-25T05:07:33Z","body":"Update to this issue - after the last couple months of testing, we've determined that UniProt's SwissProt and UniRef90 are effective references depending on the work being performed.  We've added UniRef90 as a standard option to the prepare command, and also added the option to prepare a reference post-indexing in case someone indexes manually and skips the prepare command.  \r\n\r\nAlso, since preparing is a custom tailored process per reference (since some specific cleanup is needed depending on the reference type, e.g. UniRef90), we've kept it specific to these two reference databases for now - but if anyone using PALADIN in the future finds a reference database that works well and you feel it would be a helpful addition for other users, please don't hesitate to let us know.  Closing this for now.  "}}