{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3353","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3353/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3353/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3353/events","html_url":"https://github.com/galaxyproject/galaxy/issues/3353","id":197002901,"number":3353,"title":"Samtools Filter on BAM or SAM fails at http://usegalaxy.org","user":{"login":"jennaj","id":8999735,"avatar_url":"https://avatars.githubusercontent.com/u/8999735?v=3","gravatar_id":"","url":"https://api.github.com/users/jennaj","html_url":"https://github.com/jennaj","followers_url":"https://api.github.com/users/jennaj/followers","following_url":"https://api.github.com/users/jennaj/following{/other_user}","gists_url":"https://api.github.com/users/jennaj/gists{/gist_id}","starred_url":"https://api.github.com/users/jennaj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennaj/subscriptions","organizations_url":"https://api.github.com/users/jennaj/orgs","repos_url":"https://api.github.com/users/jennaj/repos","events_url":"https://api.github.com/users/jennaj/events{/privacy}","received_events_url":"https://api.github.com/users/jennaj/received_events","type":"User","site_admin":false},"labels":[{"id":483773323,"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/area/tool-dependencies","name":"area/tool-dependencies","color":"006b75","default":false},{"id":180024669,"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/kind/bug","name":"kind/bug","color":"84b6eb","default":false},{"id":276600485,"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/triage","name":"triage","color":"e11d21","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-21T18:35:01Z","updated_at":"2016-12-22T15:05:54Z","closed_at":null,"body":"Fails immediately. Was a problem last week, then worked, now fails again on some runs, but not all. Same exact inputs.\r\n\r\n**Error**:\r\n\r\n> Job environment and execution information is available at the job Info Page.\r\n> Job ID\tXXX\r\n> Tool ID\ttoolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2\r\n> Tool Version\t1.1.2\r\n> Job PID or DRM id\tNone\r\n> Job Tool Version\tNone\r\n> Job Execution and Failure Information\r\n\r\n> Command Line\r\n> \r\n> None\r\n> stderr\r\n> \r\n> \r\n> stdout\r\n> \r\n> \r\n> Job Information\r\n> \r\n> Can't instantiate abstract class SafeStringWrapper(galaxy.datatypes.tabular.TabularData:<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'galaxy.util.object_wrapper.SafeStringWrapper'>,<class 'numbers.Number'>,<type 'NoneType'>,<type 'NotI\r\n> Job Traceback\r\n> \r\n> Traceback (most recent call last):\r\n>   File \"/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/__init__.py\", line 170, in prepare_job\r\n>     job_wrapper.prepare()\r\n>   File \"/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py\", line 909, in prepare\r\n>     self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()\r\n>   File \"/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py\", line 445, in build\r\n>     raise e\r\n> TypeError: Can't instantiate abstract class SafeStringWrapper(galaxy.datatypes.tabular.TabularData:<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'galaxy.util.object_wrapper.SafeStringWrapper'>,<class 'numbers.Number'>,<type 'NoneType'>,<type 'NotImplementedType'>,<type 'bool'>,<type 'bytearray'>,<type 'ellipsis'>) with abstract methods set_meta\r\n\r\ncc @galaxyproject/guac @natefoo "},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/268817981","html_url":"https://github.com/galaxyproject/galaxy/issues/3353#issuecomment-268817981","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3353","id":268817981,"user":{"login":"natefoo","id":286969,"avatar_url":"https://avatars.githubusercontent.com/u/286969?v=3","gravatar_id":"","url":"https://api.github.com/users/natefoo","html_url":"https://github.com/natefoo","followers_url":"https://api.github.com/users/natefoo/followers","following_url":"https://api.github.com/users/natefoo/following{/other_user}","gists_url":"https://api.github.com/users/natefoo/gists{/gist_id}","starred_url":"https://api.github.com/users/natefoo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/natefoo/subscriptions","organizations_url":"https://api.github.com/users/natefoo/orgs","repos_url":"https://api.github.com/users/natefoo/repos","events_url":"https://api.github.com/users/natefoo/events{/privacy}","received_events_url":"https://api.github.com/users/natefoo/received_events","type":"User","site_admin":false},"created_at":"2016-12-22T15:05:54Z","updated_at":"2016-12-22T15:05:54Z","body":"This is a new bug since upgrading to 16.10 and I don't really have any immediate ideas on what's causing it. Does anyone know if any command line generation stuff has changed? @jmchilton?"}}
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