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mvdbeek
64e74b8b48
Fixes https://sentry.galaxyproject.org/share/issue/5b8d495edd6545278d4d93d0ed69ac3a/: ``` Message Uncaught exception in exposed API method: Stack Trace Newest gaierror: [Errno -2] Name or service not known File "urllib3/connection.py", line 174, in _new_conn conn = connection.create_connection( File "urllib3/util/connection.py", line 72, in create_connection for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): File "socket.py", line 962, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known File "urllib3/connectionpool.py", line 715, in urlopen httplib_response = self._make_request( File "urllib3/connectionpool.py", line 416, in _make_request conn.request(method, url, **httplib_request_kw) File "urllib3/connection.py", line 244, in request super(HTTPConnection, self).request(method, url, body=body, headers=headers) File "http/client.py", line 1286, in request self._send_request(method, url, body, headers, encode_chunked) File "http/client.py", line 1332, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "http/client.py", line 1281, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "http/client.py", line 1041, in _send_output self.send(msg) File "http/client.py", line 979, in send self.connect() File "urllib3/connection.py", line 205, in connect conn = self._new_conn() File "urllib3/connection.py", line 186, in _new_conn raise NewConnectionError( MaxRetryError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known')) File "requests/adapters.py", line 486, in send resp = conn.urlopen( File "urllib3/connectionpool.py", line 799, in urlopen retries = retries.increment( File "urllib3/util/retry.py", line 592, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) ConnectionError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known')) File "galaxy/web/framework/decorators.py", line 346, in decorator rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/api/workflows.py", line 261, in create archive_data = server.get_version_descriptor(trs_tool_id, trs_version_id) File "galaxy/workflow/trs_proxy.py", line 115, in get_version_descriptor return self._get(trs_api_url)["content"] File "galaxy/workflow/trs_proxy.py", line 126, in _get response = requests.get(url, params=params, timeout=DEFAULT_SOCKET_TIMEOUT) File "galaxy/util/requests.py", line 29, in wrapper rval = f(*args, **kwargs) File "requests/api.py", line 73, in get return request("get", url, params=params, **kwargs) File "requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) File "requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) File "requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) File "requests/adapters.py", line 519, in send raise ConnectionError(e, request=request) ``` which happened for https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url=http%3A%2F%2Flocalhost%3A4000%2F%2Ftraining-material%2F%2Fapi%2Fga4gh%2Ftrs%2Fv2%2Ftools%2Fvariant-analysis-microbial-variants%2Fversions%2Fmicrobial_variant_calling"
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
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:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
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:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
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:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.8 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.8.18
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .