{"action":"opened","issue":{"url":"https://api.github.com/repos/timbitz/aligater/issues/1","repository_url":"https://api.github.com/repos/timbitz/aligater","labels_url":"https://api.github.com/repos/timbitz/aligater/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/timbitz/aligater/issues/1/comments","events_url":"https://api.github.com/repos/timbitz/aligater/issues/1/events","html_url":"https://github.com/timbitz/aligater/issues/1","id":162895913,"number":1,"title":"hgSQLBasics missing?","user":{"login":"riasc","id":8933304,"avatar_url":"https://avatars.githubusercontent.com/u/8933304?v=3","gravatar_id":"","url":"https://api.github.com/users/riasc","html_url":"https://github.com/riasc","followers_url":"https://api.github.com/users/riasc/followers","following_url":"https://api.github.com/users/riasc/following{/other_user}","gists_url":"https://api.github.com/users/riasc/gists{/gist_id}","starred_url":"https://api.github.com/users/riasc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/riasc/subscriptions","organizations_url":"https://api.github.com/users/riasc/orgs","repos_url":"https://api.github.com/users/riasc/repos","events_url":"https://api.github.com/users/riasc/events{/privacy}","received_events_url":"https://api.github.com/users/riasc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-06-29T10:48:24Z","updated_at":"2016-06-29T10:48:24Z","closed_at":null,"body":"Hello,\r\nas I'm working on something similar, so `aligater` caught my attention. I was trying to reproduce the analysis with aligater, but somehow couldn't get it to work with the default parameters. The `hgSQLBasics` module seems to be missing at it is in the `intRagenic` repository. Or what am I missing? Just piping the results from `aligater align` should be sufficient? Also I can't get any usage information on the specific aligater steps with `-h`, e.g., `aligater detect -h` but I guess thats still to come. \r\n\r\nCheers.\r\nRichard"}}
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