{"action":"created","issue":{"url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/196","repository_url":"https://api.github.com/repos/ARTbio/GalaxyKickStart","labels_url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/196/labels{/name}","comments_url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/196/comments","events_url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/196/events","html_url":"https://github.com/ARTbio/GalaxyKickStart/pull/196","id":177306568,"number":196,"title":"upgrade change set to release_16.07","user":{"login":"drosofff","id":11705625,"avatar_url":"https://avatars.githubusercontent.com/u/11705625?v=3","gravatar_id":"","url":"https://api.github.com/users/drosofff","html_url":"https://github.com/drosofff","followers_url":"https://api.github.com/users/drosofff/followers","following_url":"https://api.github.com/users/drosofff/following{/other_user}","gists_url":"https://api.github.com/users/drosofff/gists{/gist_id}","starred_url":"https://api.github.com/users/drosofff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drosofff/subscriptions","organizations_url":"https://api.github.com/users/drosofff/orgs","repos_url":"https://api.github.com/users/drosofff/repos","events_url":"https://api.github.com/users/drosofff/events{/privacy}","received_events_url":"https://api.github.com/users/drosofff/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-09-15T22:35:01Z","updated_at":"2016-09-16T10:12:05Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/pulls/196","html_url":"https://github.com/ARTbio/GalaxyKickStart/pull/196","diff_url":"https://github.com/ARTbio/GalaxyKickStart/pull/196.diff","patch_url":"https://github.com/ARTbio/GalaxyKickStart/pull/196.patch"},"body":"- upgrade to release_16.07 in group_vars/all\r\n- set use of tool_sheds_conf.xml in group_vars/all\r\n- set conda use in group_vars/all"},"comment":{"url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/comments/247565663","html_url":"https://github.com/ARTbio/GalaxyKickStart/pull/196#issuecomment-247565663","issue_url":"https://api.github.com/repos/ARTbio/GalaxyKickStart/issues/196","id":247565663,"user":{"login":"drosofff","id":11705625,"avatar_url":"https://avatars.githubusercontent.com/u/11705625?v=3","gravatar_id":"","url":"https://api.github.com/users/drosofff","html_url":"https://github.com/drosofff","followers_url":"https://api.github.com/users/drosofff/followers","following_url":"https://api.github.com/users/drosofff/following{/other_user}","gists_url":"https://api.github.com/users/drosofff/gists{/gist_id}","starred_url":"https://api.github.com/users/drosofff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drosofff/subscriptions","organizations_url":"https://api.github.com/users/drosofff/orgs","repos_url":"https://api.github.com/users/drosofff/repos","events_url":"https://api.github.com/users/drosofff/events{/privacy}","received_events_url":"https://api.github.com/users/drosofff/received_events","type":"User","site_admin":false},"created_at":"2016-09-16T10:12:05Z","updated_at":"2016-09-16T10:12:05Z","body":"Humm, tail-f uwsgi.log loops and complain:\r\n```\r\nmigrate.versioning.script.base DEBUG 2016-09-16 10:07:18,131 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py...\r\nmigrate.versioning.script.base DEBUG 2016-09-16 10:07:18,131 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully\r\nmigrate.versioning.repository DEBUG 2016-09-16 10:07:18,132 Repository lib/tool_shed/galaxy_install/migrate loaded successfully\r\nmigrate.versioning.repository DEBUG 2016-09-16 10:07:18,132 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])\r\nTraceback (most recent call last):\r\n  File \"lib/galaxy/webapps/galaxy/buildapp.py\", line 55, in paste_app_factory\r\n    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )\r\n  File \"lib/galaxy/app.py\", line 64, in __init__\r\n    self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )\r\n  File \"lib/galaxy/config.py\", line 921, in _configure_models\r\n    verify_tools( self, install_db_url, config_file, install_database_options )\r\n  File \"lib/tool_shed/galaxy_install/migrate/check.py\", line 43, in verify_tools\r\n    latest_tool_migration_script_number )\r\n  File \"lib/tool_shed/util/common_util.py\", line 34, in check_for_missing_tools\r\n    tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, tool_shed )\r\n  File \"lib/tool_shed/util/common_util.py\", line 236, in get_tool_shed_url_from_tool_shed_registry\r\n    for shed_url in app.tool_shed_registry.tool_sheds.values():\r\nAttributeError: 'NoneType' object has no attribute 'tool_sheds'\r\nFri Sep 16 10:07:24 2016 - *** Starting uWSGI 2.0.13.1 (64bit) on [Fri Sep 16 10:07:24 2016] ***\r\nFri Sep 16 10:07:24 2016 - compiled with version: 4.8.4 on 16 September 2016 10:05:45\r\nFri Sep 16 10:07:24 2016 - os: Linux-3.13.0-65-generic #106-Ubuntu SMP Fri Oct 2 22:08:27 UTC 2015\r\nFri Sep 16 10:07:24 2016 - nodename: vm0062\r\nFri Sep 16 10:07:24 2016 - machine: x86_64\r\nFri Sep 16 10:07:24 2016 - clock source: unix\r\nFri Sep 16 10:07:24 2016 - detected number of CPU cores: 4\r\nFri Sep 16 10:07:24 2016 - current working directory: /home/galaxy/galaxy\r\nFri Sep 16 10:07:24 2016 - detected binary path: /home/galaxy/galaxy/.venv/bin/uwsgi\r\nFri Sep 16 10:07:24 2016 - !!! no internal routing support, rebuild with pcre support !!!\r\nFri Sep 16 10:07:24 2016 - your processes number limit is 63647\r\nFri Sep 16 10:07:24 2016 - your memory page size is 4096 bytes\r\nFri Sep 16 10:07:24 2016 - detected max file descriptor number: 1024\r\nFri Sep 16 10:07:24 2016 - lock engine: pthread robust mutexes\r\nFri Sep 16 10:07:24 2016 - thunder lock: disabled (you can enable it with --thunder-lock)\r\nFri Sep 16 10:07:24 2016 - uwsgi socket 0 bound to TCP address 127.0.0.1:4001 fd 3\r\nFri Sep 16 10:07:24 2016 - Python version: 2.7.6 (default, Jun 22 2015, 18:01:27)  [GCC 4.8.2]\r\nFri Sep 16 10:07:24 2016 - Set PythonHome to /home/galaxy/galaxy/.venv\r\nFri Sep 16 10:07:24 2016 - Python main interpreter initialized at 0x22e5390\r\nFri Sep 16 10:07:24 2016 - python threads support enabled\r\nFri Sep 16 10:07:24 2016 - your server socket listen backlog is limited to 100 connections\r\nFri Sep 16 10:07:24 2016 - your mercy for graceful operations on workers is 60 seconds\r\nFri Sep 16 10:07:24 2016 - mapped 166144 bytes (162 KB) for 2 cores\r\nFri Sep 16 10:07:24 2016 - *** Operational MODE: threaded ***\r\nFri Sep 16 10:07:24 2016 - added lib/ to pythonpath.\r\nFri Sep 16 10:07:24 2016 - Loading paste environment: config:/home/galaxy/galaxy/config/galaxy.ini\r\nDEBUG:galaxy.app:python path is: lib/, ., , /home/galaxy/galaxy/.venv/lib/python2.7, /home/galaxy/galaxy/.venv/lib/python2.7/plat-x86_64-linux-gnu, /home/galaxy/galaxy/.venv/lib/python2.7/lib-tk, /home/galaxy/galaxy/.venv/lib/python2.7/lib-old, /home/galaxy/galaxy/.venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages\r\nINFO:galaxy.config:Logging at '10' level to 'stdout'\r\ngalaxy.queue_worker INFO 2016-09-16 10:07:26,254 Initializing main Galaxy Queue Worker on sqlalchemy+postgresql://galaxy:********@localhost:5432/galaxy?client_encoding=utf8\r\ngalaxy.app DEBUG 2016-09-16 10:07:26,276 Using \"galaxy.ini\" config file: /home/galaxy/galaxy/config/galaxy.ini\r\nmigrate.versioning.repository DEBUG 2016-09-16 10:07:26,310 Loading repository lib/galaxy/model/migrate...\r\n```\r\n"}}
{"actor":{"display_login":"drosofff"}}