Dear all, I've been getting this error for a few days now, it basically prevents anything from being installed on the first go. Individual tools can be installed, but even then I have to try multiple times.
Any ideas how to fix this? Cheers, Christopher The details from galaxy.log are (installing an older VCFtools package): 172.22.24.119 - - [10/Jul/2019:10:44:32 +0200] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install?change set_revisions=34a6b690e4b5&repository_ids=2ba42187f2588c4b&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" galaxy.tools.toolbox.base DEBUG 2019-07-10 10:44:55,592 Appending to tool panel section: NGS:VCFtools 172.22.24.119 - - [10/Jul/2019:10:44:58 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" 172.22.24.119 - - [10/Jul/2019:10:45:01 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" 172.22.24.119 - - [10/Jul/2019:10:44:55 +0200] "POST /admin_toolshed/install_repositories HTTP/1.1" 500 - "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install"; "Moz illa/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" *Error - <type 'exceptions.OSError'>: inotify instance limit reached* URL: http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/install_repositories File '/opt/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 143 in __call__ return self.handle_request(environ, start_response) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 222 in handle_request body = method(trans, **kwargs) File '/opt/galaxy/galaxy/lib/galaxy/web/framework/decorators.py', line 101 in decorator return func(self, trans, *args, **kwargs) File '/opt/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 575 in install_repositories reinstalling=reinstalling, File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 846 in install_repositories tool_panel_section_mapping=tool_panel_section_mapping) File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 893 in install_tool_shed_repository tool_panel_section_mapping=tool_panel_section_mapping) File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 544 in __handle_repository_contents repository_tools_tups = irmm.get_repository_tools_tups() File '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 75 in get_repository_tools_tups tool = self.app.toolbox.load_tool(os.path.abspath(load_relative_path), guid=guid, use_cached=False) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/base.py', line 766 in load_tool self.watch_tool(tool) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/base.py', line 774 in watch_tool self._tool_watcher.watch_file(tool.config_file, tool.id) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py', line 198 in watch_file self.monitor(tool_dir) File '/opt/galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py', line 190 in monitor self.observer.schedule(self.event_handler, dir, recursive=False) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py', line 293 in schedule emitter.start() File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/utils/__init__.py', line 110 in start self.on_thread_start() File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify.py', line 121 in on_thread_start self._inotify = InotifyBuffer(path, self.watch.is_recursive) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_buffer.py', line 35 in __init__ self._inotify = Inotify(path, recursive) File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_c.py', line 188 in __init__ Inotify._raise_error() *File '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/inotify_c.py', line 415 in _raise_error** ** raise OSError("inotify instance limit reached")** **OSError: inotify instance limit reached** * CGI Variables ------------- CONTENT_LENGTH: '12169' CONTENT_TYPE: 'application/x-www-form-urlencoded; charset=UTF-8' HTTP_ACCEPT: 'text/html, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e' HTTP_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de' HTTP_REFERER: 'http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0' HTTP_X_FORWARDED_FOR: '172.22.24.119' HTTP_X_FORWARDED_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de' HTTP_X_FORWARDED_SERVER: 'fe80::216:3eff:fe80:c02b' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' ORGINAL_HTTP_HOST: 'localhost:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/admin_toolshed/install_repositories' REMOTE_ADDR: '172.22.24.119' REQUEST_METHOD: 'POST' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f9f48207410> controller_action_key: u'web.admin_toolshed.install_repositories' is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e'>, 'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f9f48c86fd0> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f9f486fcd90> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'fd8cc98ea2ee11e9a89100163e80c02b' webob._body_file: (<_io.BufferedReader>, <socket._fileobject object at 0x7f9f3a4b5ad0 length=12169>) webob._parsed_post_vars: (MultiDict([('tool_shed_repository_ids', u"[u'ac218635d795e337', u'e3e09dfaa8fad8c8', u'1efe9eb0bff40152', u'358d8704ef89cb6b', u'cbc5119f47881258']"), ('encoded_kwd', u'59b03a7799b953da9827424b9cef2236c5b9f461: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... 0x7f9f35cdfed0>) webob._parsed_query_vars: (GET([]), '') webob.is_body_seekable: True wsgi process: 'Multithreaded' wsgi.input_terminated: True -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.prev...@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. 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