{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/452","repository_url":"https://api.github.com/repos/galaxyproject/tools-devteam","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/452/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/452/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/452/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/452","id":208216432,"number":452,"title":"cufflinks dependency problem","user":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2017-02-16T19:09:10Z","updated_at":"2017-02-17T21:13:54Z","closed_at":null,"body":"I just installed a brand new galaxy server (16.10). I installed cufflinks from scratch.\r\n\r\nI am having a bug when running the code:\r\n\r\n```\r\nFatal error: Exit code 1 ()\r\nTraceback (most recent call last):\r\n  File \"/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/83bec71c5c9f/cufflinks/cufflinks_wrapper.py\", line 10, in <module>\r\n    from galaxy.datatypes.util.gff_util import gff_attributes_to_str, parse_gff_attributes\r\n  File \"/galaxy-central/lib/galaxy/datatypes/util/gff_util.py\", line 6, in <module>\r\n    from bx.intervals.io import GenomicInterval, MissingFieldError, NiceReaderWrapper, ParseError, GenomicIntervalReader\r\nImportError: No module named 'bx'`\r\n\r\n```\r\n\r\nNow, I have tracked the dependency definition and bx is included and seems perfectly correct.\r\n\r\nIt seems that the wrapper is calling a conda-based python, which has a\r\n\r\n```\r\n/export/tool_deps/_conda/envs/__bx-python@0.7.3/bin/python\r\n```\r\n\r\ninside.\r\n\r\nBut for some reason the bx package is not being made available in the environment being run by cufflinks.\r\n\r\nThis is a brand new installation and I suspect that there are no strange interactions or ugly hacks at this stage."},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/comments/280768049","html_url":"https://github.com/galaxyproject/tools-devteam/issues/452#issuecomment-280768049","issue_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/452","id":280768049,"user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars.githubusercontent.com/u/6804901?v=3","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"created_at":"2017-02-17T21:13:54Z","updated_at":"2017-02-17T21:13:54Z","body":"Cufflinks is one of the tools that needs Galaxy's python currently, because it imports from the datatypes. You shouldn't get the same error on 17.01 and 16.10 though. This tool can currently be used only with toolshed package dependencies, are they installed? We'll have to upgrade this to support conda and remove the import from galaxy's codebase."}}
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