Thank you very much! We have 19.01 running and the parameter that I had to put to "false" was "watch_tools" All the best, Christopher On 7/10/19 12:00 PM, Marius van den Beek wrote:

Hi Christopher,

you might want to turn off `watch_tools` if you are using it, this is only needed when using the pretty-much undocumented feature where you dump tools into a directory without registering them in any tool_conf.xml file. All other tool reloading happens by another means.

Similarly, if you're using 19.05 and you don't manipulate the tool data table entries manually you can disable `watch_tool_data_dir`.

Finally this is usually a sign of allocating too many processes and threads for your webservers/handlers/mules, as each one starts their own watchdog. A common misconception is that this makes Galaxy run faster. but it actually just increases the amount of concurrent requests Galaxy can handle.

Best, Marius

On Wed, 10 Jul 2019 at 11:43, Previti <christopher.previti@dkfz-heidelberg.de <mailto:christopher.previti@dkfz-heidelberg.de>> wrote:

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... set_revisions=34a6b690e4b5&repository_ids=2ba42187f2588c4b&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F <http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install?changeset_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_repositorie... 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 <http://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://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://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.previti@dkfz.de <mailto:christopher.previti@dkfz.de> <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de> <http://www.dkfz.de/>

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-- *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.previti@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. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.