{"action":"created","issue":{"url":"https://api.github.com/repos/naturalis/supersmart/issues/77","labels_url":"https://api.github.com/repos/naturalis/supersmart/issues/77/labels{/name}","comments_url":"https://api.github.com/repos/naturalis/supersmart/issues/77/comments","events_url":"https://api.github.com/repos/naturalis/supersmart/issues/77/events","html_url":"https://github.com/naturalis/supersmart/issues/77","id":99532113,"number":77,"title":"smrt classify needed? ","user":{"login":"hettling","id":4069510,"avatar_url":"https://avatars.githubusercontent.com/u/4069510?v=3","gravatar_id":"","url":"https://api.github.com/users/hettling","html_url":"https://github.com/hettling","followers_url":"https://api.github.com/users/hettling/followers","following_url":"https://api.github.com/users/hettling/following{/other_user}","gists_url":"https://api.github.com/users/hettling/gists{/gist_id}","starred_url":"https://api.github.com/users/hettling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hettling/subscriptions","organizations_url":"https://api.github.com/users/hettling/orgs","repos_url":"https://api.github.com/users/hettling/repos","events_url":"https://api.github.com/users/hettling/events{/privacy}","received_events_url":"https://api.github.com/users/hettling/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/naturalis/supersmart/labels/analysis","name":"analysis","color":"f7c6c7"},{"url":"https://api.github.com/repos/naturalis/supersmart/labels/question","name":"question","color":"cc317c"}],"state":"closed","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/naturalis/supersmart/milestones/2","html_url":"https://github.com/naturalis/supersmart/milestones/v2.0","labels_url":"https://api.github.com/repos/naturalis/supersmart/milestones/2/labels","id":1065159,"number":2,"title":"v2.0","description":"Milestone for all the enhancements that are deferred till after v1.0. For now this may become a gathering place for all blue sky thinking about things such as:\r\n* automatic harvesting of fossil calibrations through a web service API: this functionality simply doesn't exist yet so there is no client for us to write.\r\n* recursive inference: this constitutes a pretty big enhancement/rewrite which we don't yet need for the scale at which we are working now, but it'll become important later down the line.\r\n* inclusion of NGS data: too much work for now, defer.","creator":{"login":"rvosa","id":106490,"avatar_url":"https://avatars.githubusercontent.com/u/106490?v=3","gravatar_id":"","url":"https://api.github.com/users/rvosa","html_url":"https://github.com/rvosa","followers_url":"https://api.github.com/users/rvosa/followers","following_url":"https://api.github.com/users/rvosa/following{/other_user}","gists_url":"https://api.github.com/users/rvosa/gists{/gist_id}","starred_url":"https://api.github.com/users/rvosa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rvosa/subscriptions","organizations_url":"https://api.github.com/users/rvosa/orgs","repos_url":"https://api.github.com/users/rvosa/repos","events_url":"https://api.github.com/users/rvosa/events{/privacy}","received_events_url":"https://api.github.com/users/rvosa/received_events","type":"User","site_admin":false},"open_issues":13,"closed_issues":5,"state":"open","created_at":"2015-04-13T14:26:30Z","updated_at":"2015-08-11T13:34:26Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2015-08-06T21:50:47Z","updated_at":"2015-08-11T13:34:26Z","closed_at":"2015-08-11T13:34:26Z","body":"Just wondering if the second pipeline step `smrt` classify is redundant or not. We use the NCBI classification tree in two special cases: \r\n* in `smrt bbinfer` as a starting tree, but only if the inference tool is examl\r\n* in `smrt bbdecompose`, but only if outgroups for the clades are automatically chosen with `-g` flag.\r\n\r\nThe classification tree does not provide any more information than the taxa table. Although it can be nice to look at, I was wondering if generating this tree should be removed to not frighten the users with so many subcommands.."},"comment":{"url":"https://api.github.com/repos/naturalis/supersmart/issues/comments/129875148","html_url":"https://github.com/naturalis/supersmart/issues/77#issuecomment-129875148","issue_url":"https://api.github.com/repos/naturalis/supersmart/issues/77","id":129875148,"user":{"login":"hettling","id":4069510,"avatar_url":"https://avatars.githubusercontent.com/u/4069510?v=3","gravatar_id":"","url":"https://api.github.com/users/hettling","html_url":"https://github.com/hettling","followers_url":"https://api.github.com/users/hettling/followers","following_url":"https://api.github.com/users/hettling/following{/other_user}","gists_url":"https://api.github.com/users/hettling/gists{/gist_id}","starred_url":"https://api.github.com/users/hettling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hettling/subscriptions","organizations_url":"https://api.github.com/users/hettling/orgs","repos_url":"https://api.github.com/users/hettling/repos","events_url":"https://api.github.com/users/hettling/events{/privacy}","received_events_url":"https://api.github.com/users/hettling/received_events","type":"User","site_admin":false},"created_at":"2015-08-11T13:34:26Z","updated_at":"2015-08-11T13:34:26Z","body":"`smrt classify` is now removed from the pipeline."}}