{"action":"created","issue":{"url":"https://api.github.com/repos/epigen/looper/issues/46","repository_url":"https://api.github.com/repos/epigen/looper","labels_url":"https://api.github.com/repos/epigen/looper/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/epigen/looper/issues/46/comments","events_url":"https://api.github.com/repos/epigen/looper/issues/46/events","html_url":"https://github.com/epigen/looper/pull/46","id":208279295,"number":46,"title":"No more null logger","user":{"login":"vreuter","id":12036370,"avatar_url":"https://avatars.githubusercontent.com/u/12036370?v=3","gravatar_id":"","url":"https://api.github.com/users/vreuter","html_url":"https://github.com/vreuter","followers_url":"https://api.github.com/users/vreuter/followers","following_url":"https://api.github.com/users/vreuter/following{/other_user}","gists_url":"https://api.github.com/users/vreuter/gists{/gist_id}","starred_url":"https://api.github.com/users/vreuter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vreuter/subscriptions","organizations_url":"https://api.github.com/users/vreuter/orgs","repos_url":"https://api.github.com/users/vreuter/repos","events_url":"https://api.github.com/users/vreuter/events{/privacy}","received_events_url":"https://api.github.com/users/vreuter/received_events","type":"User","site_admin":false},"labels":[{"id":371660136,"url":"https://api.github.com/repos/epigen/looper/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/epigen/looper/milestones/2","html_url":"https://github.com/epigen/looper/milestone/2","labels_url":"https://api.github.com/repos/epigen/looper/milestones/2/labels","id":2277568,"number":2,"title":"0.4","description":"","creator":{"login":"nsheff","id":5271009,"avatar_url":"https://avatars.githubusercontent.com/u/5271009?v=3","gravatar_id":"","url":"https://api.github.com/users/nsheff","html_url":"https://github.com/nsheff","followers_url":"https://api.github.com/users/nsheff/followers","following_url":"https://api.github.com/users/nsheff/following{/other_user}","gists_url":"https://api.github.com/users/nsheff/gists{/gist_id}","starred_url":"https://api.github.com/users/nsheff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsheff/subscriptions","organizations_url":"https://api.github.com/users/nsheff/orgs","repos_url":"https://api.github.com/users/nsheff/repos","events_url":"https://api.github.com/users/nsheff/events{/privacy}","received_events_url":"https://api.github.com/users/nsheff/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":2,"state":"open","created_at":"2017-01-25T16:05:12Z","updated_at":"2017-02-17T01:16:45Z","due_on":"2017-02-16T08:00:00Z","closed_at":null},"comments":3,"created_at":"2017-02-16T23:15:25Z","updated_at":"2017-02-17T02:56:12Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/epigen/looper/pulls/46","html_url":"https://github.com/epigen/looper/pull/46","diff_url":"https://github.com/epigen/looper/pull/46.diff","patch_url":"https://github.com/epigen/looper/pull/46.patch"},"body":"The test case that you provided now runs through on Rivanna @nsheff as a \"Dry run\" for ATAC and skipping other protocols since they're not defined in the associated protocol mappings file. I had to copy a few project files, tweak some paths and variables in the config, and copy over the data files to run this through from my account, as there were some write/read permissions issues since some items were referencing your user paths. Thus, there are several failure points so I'd be more comfortable with this if you can run that test case as you were earlier and validate it against your expectation after a `pip install --upgrade` from my fork's `fix_master` branch.\r\nFix https://github.com/epigen/looper/issues/44"},"comment":{"url":"https://api.github.com/repos/epigen/looper/issues/comments/280535508","html_url":"https://github.com/epigen/looper/pull/46#issuecomment-280535508","issue_url":"https://api.github.com/repos/epigen/looper/issues/46","id":280535508,"user":{"login":"nsheff","id":5271009,"avatar_url":"https://avatars.githubusercontent.com/u/5271009?v=3","gravatar_id":"","url":"https://api.github.com/users/nsheff","html_url":"https://github.com/nsheff","followers_url":"https://api.github.com/users/nsheff/followers","following_url":"https://api.github.com/users/nsheff/following{/other_user}","gists_url":"https://api.github.com/users/nsheff/gists{/gist_id}","starred_url":"https://api.github.com/users/nsheff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsheff/subscriptions","organizations_url":"https://api.github.com/users/nsheff/orgs","repos_url":"https://api.github.com/users/nsheff/repos","events_url":"https://api.github.com/users/nsheff/events{/privacy}","received_events_url":"https://api.github.com/users/nsheff/received_events","type":"User","site_admin":false},"created_at":"2017-02-17T02:56:12Z","updated_at":"2017-02-17T02:56:12Z","body":"Now it does complete, so some stuff is fixed. \r\n\r\nBut there are a few things still...\r\n\r\n- The logger messages appear to not be recognized by `less` the way I expected...does it have to do with outputting to stderr vs stdout?\r\n- it's not spitting out the right information that it used to; e.g. \r\n`2017-02-16 21:51:25,906 looper.looper looper : 236 - [ERROR] > \r\nNot submitted: Required input files not found` \r\nIt used to say which files those were.\r\n\r\nAnd also, the input files should be found, so this hasn't solved #45, for example.\r\n\r\n"}}
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