{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423","repository_url":"https://api.github.com/repos/broadinstitute/viral-ngs","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/events","html_url":"https://github.com/broadinstitute/viral-ngs/issues/423","id":168224461,"number":423,"title":"snpEff requires LC_ALL=C","user":{"login":"haydenm","id":3084862,"avatar_url":"https://avatars.githubusercontent.com/u/3084862?v=3","gravatar_id":"","url":"https://api.github.com/users/haydenm","html_url":"https://github.com/haydenm","followers_url":"https://api.github.com/users/haydenm/followers","following_url":"https://api.github.com/users/haydenm/following{/other_user}","gists_url":"https://api.github.com/users/haydenm/gists{/gist_id}","starred_url":"https://api.github.com/users/haydenm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/haydenm/subscriptions","organizations_url":"https://api.github.com/users/haydenm/orgs","repos_url":"https://api.github.com/users/haydenm/repos","events_url":"https://api.github.com/users/haydenm/events{/privacy}","received_events_url":"https://api.github.com/users/haydenm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-07-29T00:09:30Z","updated_at":"2016-07-29T12:21:27Z","closed_at":null,"body":"`snpEff` gave me an error related to coordinates. Changing `LC_ALL` from `en_US.utf8` to `C` fixed this. The issue might relate to a use of GNU `sort`. Perhaps we can set `LC_ALL` to `C` for just the call to `snpEff`?"},"comment":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/comments/236166453","html_url":"https://github.com/broadinstitute/viral-ngs/issues/423#issuecomment-236166453","issue_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423","id":236166453,"user":{"login":"dpark01","id":8513746,"avatar_url":"https://avatars.githubusercontent.com/u/8513746?v=3","gravatar_id":"","url":"https://api.github.com/users/dpark01","html_url":"https://github.com/dpark01","followers_url":"https://api.github.com/users/dpark01/followers","following_url":"https://api.github.com/users/dpark01/following{/other_user}","gists_url":"https://api.github.com/users/dpark01/gists{/gist_id}","starred_url":"https://api.github.com/users/dpark01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpark01/subscriptions","organizations_url":"https://api.github.com/users/dpark01/orgs","repos_url":"https://api.github.com/users/dpark01/repos","events_url":"https://api.github.com/users/dpark01/events{/privacy}","received_events_url":"https://api.github.com/users/dpark01/received_events","type":"User","site_admin":false},"created_at":"2016-07-29T12:21:27Z","updated_at":"2016-07-29T12:21:27Z","body":"I'd love to have a better understanding across the board of which steps actually depend on LC_ALL for proper operation. I'm surprised that snpEff is one of them because I had no idea that Java programs would change behavior based on that variable.\n\n@tomkinsc do you remember if utf8 was required by any particular step or was it that it needed to be set to something/anything for deterministic behavior?\n\nAny place we uncover a dependency on a specific LC_ALL value for proper behavior should have a defensive unit test added that fails on a different value. For now, let's just start with snpEff and deal with specific cases as we discover them.\n"}}
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