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mvdbeek
92d4ffc77a
This broke when we started re-exporting jobs to update their command line in https://github.com/galaxyproject/galaxy/pull/12459/commits/65e0ee213ae574bc0a45dfcc60e997863ff96a7c#diff-bfb854f344e56a25a86761f80a639de09add404a7a53ebde45afb908762fc1eaR161: ``` ERROR galaxy.jobs:__init__.py:1836 problem importing job outputs. stdout [] stderr [ Traceback (most recent call last): File "metadata/set.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 121, in set_metadata set_metadata_portable() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 307, in set_metadata_portable export_store.export_job(job, include_job_data=False) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 1320, in export_job self.export_jobs([job], include_job_data=include_job_data) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 1336, in export_jobs job_attrs = job.serialize(self.security, self.serialization_options) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 339, in serialize return self._serialize(id_encoder, serialization_options) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 1447, in _serialize params_objects = remap(params_objects, remap_objects) File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/boltons/iterutils.py", line 1128, in remap visited_item = visit(path, key, value) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 1441, in remap_objects new_id = serialization_options.get_identifier_for_id(id_encoder, obj["id"]) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 323, in get_identifier_for_id raise NotImplementedError() NotImplementedError ] ``` To test run `GALAXY_CONFIG_METADATA_STRATEGY=extended ./run_tests.sh -api lib/galaxy_test/api/test_jobs.py::JobsApiTestCase::test_dce_submission_security`
.. 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://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.7 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.7.6
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>`_ .