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Merge pull request #485 from ewels/rename-ewels-multiqc
Rename ewels/MegaQC -> MultiQC/MegaQC
2 parents cf073f0 + 5000d45 commit d1c2ea3

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‎.github/workflows/publish_docs.yaml

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# TODO: We could also build latex & PDF documentation and upload them as artifacts
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- name: Deploy
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if: ${{ github.ref == 'refs/heads/master' }}
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if: ${{ github.ref == 'refs/heads/main' }}
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}

‎CHANGELOG.rst

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* Fix a bug in pytest where we used `scope` as a positional argument
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* Update the SubFactoryList to a new version that works with newer FactoryBoy versions
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.. _[#430]: https://github.com/ewels/MegaQC/issues/430
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.. _[#440]: https://github.com/ewels/MegaQC/pull/440
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.. _[#433]: https://github.com/ewels/MegaQC/pull/433
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.. _[#430]: https://github.com/MultiQC/MegaQC/issues/430
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.. _[#440]: https://github.com/MultiQC/MegaQC/pull/440
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.. _[#433]: https://github.com/MultiQC/MegaQC/pull/433
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=======
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- Many and more dependency updates
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.. _[#69]: https://github.com/ewels/MegaQC/issues/69
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.. _[#138]: https://github.com/ewels/MegaQC/issues/138
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.. _[#139]: https://github.com/ewels/MegaQC/issues/139
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.. _[#140]: https://github.com/ewels/MegaQC/issues/140
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.. _[#148]: https://github.com/ewels/MegaQC/issues/148
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.. _[#156]: https://github.com/ewels/MegaQC/issues/156
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.. _[#170]: https://github.com/ewels/MegaQC/issues/170
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.. _[#194]: https://github.com/ewels/MegaQC/issues/194
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.. _[#443]: https://github.com/ewels/MegaQC/pull/443
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.. _[#69]: https://github.com/MultiQC/MegaQC/issues/69
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.. _[#138]: https://github.com/MultiQC/MegaQC/issues/138
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.. _[#139]: https://github.com/MultiQC/MegaQC/issues/139
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.. _[#140]: https://github.com/MultiQC/MegaQC/issues/140
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.. _[#148]: https://github.com/MultiQC/MegaQC/issues/148
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.. _[#156]: https://github.com/MultiQC/MegaQC/issues/156
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.. _[#170]: https://github.com/MultiQC/MegaQC/issues/170
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.. _[#194]: https://github.com/MultiQC/MegaQC/issues/194
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.. _[#443]: https://github.com/MultiQC/MegaQC/pull/443

‎README.rst

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@@ -20,7 +20,7 @@ MegaQC is a web application that you can install and run on your own
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network. It collects and visualises data parsed by MultiQC across multiple runs.
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The MegaQC home page looks something like this:
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.. figure:: https://raw.githubusercontent.com/ewels/MegaQC/master/docs/source/images/megaqc_homepage.png
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.. figure:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/docs/source/images/megaqc_homepage.png
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:alt: MegaQC homepage
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Screenshot of the MegaQC home page.
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.. _MultiQC website: http://multiqc.info
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.. _GitHub repository: https://github.com/ewels/MultiQC
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.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
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.. |Docker| image:: https://img.shields.io/docker/automated/ewels/megaqc.svg?style=flat-square
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:target: https://hub.docker.com/r/ewels/megaqc/
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.. |Build Status| image:: https://travis-ci.org/ewels/MegaQC.svg?branch=master
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:target: https://travis-ci.org/ewels/MegaQC
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.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/megaqc/static/img/MegaQC_logo.png
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.. |Docker| image:: https://img.shields.io/docker/automated/multiqc/megaqc.svg?style=flat-square
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:target: https://hub.docker.com/r/multiqc/megaqc/
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.. |Gitter| image:: https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg?style=flat-square
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:target: https://gitter.im/ewels/MegaQC
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.. |Documentation| image:: https://img.shields.io/badge/Documentation-passing-passing

‎deployment/docker-compose.yml

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services:
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megaqc:
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image: ewels/megaqc
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image: multiqc/megaqc
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build: ..
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volumes:
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# Share the static files via a volume

‎docs/source/_templates/index.html

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<li class="current"><a href="index.html">Home</a></li>
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<li><a href="docs/index.html" title="Read the MegaQC documentation">Docs</a></li>
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<li><a href="http://multiqc.info/" target="_blank" title="Find out more about MultiQC, which MegaQC relies upon">MultiQC</a></li>
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<li><a href="https://gitter.im/ewels/MegaQC" target="_blank" title="Get help by chatting with the developers">Gitter</a></li>
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<li><a href="https://github.com/ewels/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
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<li><a href="https://gitter.im/MultiQC/MegaQC" target="_blank" title="Get help by chatting with the developers">Gitter</a></li>
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<li><a href="https://github.com/MultiQC/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
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</ul>
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</nav>
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<ul class="actions">
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<li><a href="docs/index.html" class="button style2">Read the docs</a></li>
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<li><a href="#" class="button style1">Try a live demo</a></li>
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<li><a href="https://github.com/ewels/MegaQC" target="_blank" class="button style2">See the code</a></li>
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<li><a href="https://github.com/MultiQC/MegaQC" target="_blank" class="button style2">See the code</a></li>
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</ul>
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</header>
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‎docs/source/conf.py

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"display_github": True,
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# Set the following variables to generate the resulting github URL for each page.
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# Format Template: https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}
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"github_user": "ewels",
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"github_user": "MultiQC",
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"github_repo": "MegaQC",
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"github_version": "master/docs",
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"github_version": "main/docs",
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"conf_py_path": "/source/",
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}
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filename = "megaqc/%s#L%d-L%d" % find_source()
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except Exception:
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filename = info["module"].replace(".", "/") + ".py"
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tag = "master"
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# TODO use this after the first release: tag = 'master' if 'dev' in release else ('v' + release)
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tag = "main"
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# TODO use this after the first release: tag = 'main' if 'dev' in release else ('v' + release)
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return "https://github.com/ewels/megaqc/blob/%s/%s" % (tag, filename)
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return "https://github.com/MultiQC/MegaQC/blob/%s/%s" % (tag, filename)

‎docs/source/docs/dev/backend.rst

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Database models are located in `model/models.py`_ and `user/models.py`_.
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Database schema migrations
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Database schema migrations
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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You need to generate a new migration whenever the database schema (ie
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.. _flask: https://www.palletsprojects.com/p/flask/
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.. _SQLAlchemy: https://docs.sqlalchemy.org/
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.. _model/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/model/models.py
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.. _user/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/user/models.py
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.. _megaqc/api: https://github.com/ewels/MegaQC/tree/master/megaqc/api
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.. _megaqc/rest_api: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api
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.. _views.py: https://github.com/ewels/MegaQC/blob/master/megaqc/rest_api/views.py
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.. _model/models.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/model/models.py
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.. _user/models.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/user/models.py
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.. _megaqc/api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api
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.. _megaqc/rest_api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/rest_api
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.. _views.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/rest_api/views.py
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.. _flapison: https://github.com/TMiguelT/flapison
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.. _schemas.py: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api/schemas.py
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.. _public/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/public/views.py
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.. _user/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/user/views.py
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.. _schemas.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/rest_api/schemas.py
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.. _public/views.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/public/views.py
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.. _user/views.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/user/views.py
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.. _Jinja2: https://jinja.palletsprojects.com/en/2.11.x/
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.. _frontend: ./frontend.md
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.. _python_tests: https://github.com/ewels/MegaQC/tree/master/tests
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.. _test_api.py: https://github.com/ewels/MegaQC/tree/master/megaqc/api/test_api.py
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.. _python_tests: https://github.com/MultiQC/MegaQC/tree/main/tests
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.. _test_api.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api/test_api.py

‎docs/source/docs/dev/documentation.rst

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The MegaQC documentation requires
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1. An installation of MegaQC to fetch the API endpoints and the Click commands.
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2. All dependencies specified in the `docs requirements.txt <https://github.com/ewels/MegaQC/blob/master/docs/requirements.txt>`_.
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Install them by invoking: ``pip install -r docs/requirements.txt``.
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2. All dependencies specified in the `docs requirements.txt <https://github.com/MultiQC/MegaQC/blob/main/docs/requirements.txt>`_.
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Install them by invoking: ``pip install -r docs/requirements.txt``.
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Publishing the documentation
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On pushes to the ``master`` branch, the documentation is automatically built and pushed
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On pushes to the ``main`` branch, the documentation is automatically built and pushed
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to the ``gh-pages`` branch. The static html files on this branch are then deployed
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to Github Pages and displayed to the outside world.
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All of this is done with the `Publish Docs Github Actions workflow <https://github.com/ewels/MegaQC/blob/master/.github/workflows/publish_docs.yaml>`.
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All of this is done with the `Publish Docs Github Actions workflow <https://github.com/MultiQC/MegaQC/blob/main/.github/workflows/publish_docs.yaml>`.

‎docs/source/docs/dev/frontend.rst

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.. _React: https://reactjs.org/
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.. _templates: https://github.com/ewels/MegaQC/tree/master/megaqc/templates
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.. _static: https://github.com/ewels/MegaQC/tree/master/megaqc/static
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.. _react.html: https://github.com/ewels/MegaQC/tree/master/megaqc/templates/public/react.html
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.. _src: https://github.com/ewels/MegaQC/tree/master/src
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.. _templates: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates
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.. _static: https://github.com/MultiQC/MegaQC/tree/main/megaqc/static
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.. _react.html: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates/public/react.html
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.. _src: https://github.com/MultiQC/MegaQC/tree/main/src

‎docs/source/docs/index.rst

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* :ref:`modindex`
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* :ref:`search`
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.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
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.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/megaqc/static/img/MegaQC_logo.png

‎docs/source/docs/installation/installation_dev.rst

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.. code:: bash
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2. Install Dependencies
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------------------------------------------------

‎docs/source/docs/installation/installation_docker.rst

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Overview
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~~~~~~~~~~
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The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_
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The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_
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to compile all Javascript scripts and the `Gunicorn Flask container <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_
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providing Gunicorn, Flask and MegaQC preconfigured for production deployments.
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The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container
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The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container
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Pulling the docker image from dockerhub
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docker run -p 80:80 multiqc/megaqc
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docker build . -t multiqc/megaqc
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docker run -p 80:80 multiqc/megaqc
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~~~~~~~~~~~~~~~
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Besides the sections below it is also recommended to read the
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Besides the sections below it is also recommended to read the
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`Gunicorn Flask container documentation <https://github.com/tiangolo/meinheld-gunicorn-flask-docker>`_,
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which explains how to customize the ``host`` IP where Gunicorn listens
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docker run -e DB_PASS=someotherpassword multiqc/megaqc
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docker run -p 80:80 multiqc/megaqc:v0.2.0
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docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql -v pg_logs:/var/log/postgresql multiqc/megaqc
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The `docker-compose`_ configuration can be accessed in the `deployment folder`_.
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a `postgres container <https://hub.docker.com/_/postgres>`_ for the SQL database
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together with the associated `.env <https://github.com/MultiQC/MegaQC/blob/main/deployment/.env>`_ file
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are found. To spin up all containers simply run from inside the `deployment folder <https://github.com/MultiQC/MegaQC/blob/main/deployment>`_:
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are defined inside the `.env <https://github.com/MultiQC/MegaQC/blob/main/deployment/.env>`_ file.
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.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
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.. _docker-compose: https://github.com/ewels/MegaQC/blob/master/deployment/docker-compose.yml
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.. _dockerhub: https://hub.docker.com/r/ewels/megaqc/
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.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/main/deployment
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.. _docker-compose: https://github.com/MultiQC/MegaQC/blob/main/deployment/docker-compose.yml
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.. _dockerhub: https://hub.docker.com/r/multiqc/megaqc/
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HTTPS
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~~~~~
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After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.
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After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.

‎docs/source/docs/installation/installation_prod.rst

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This section explains how to set up a production environment without
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containerized environment please refer to :ref:`docker_installation`.
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the usage of container technologies. If you want to run MegaQC in a
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containerized environment please refer to :ref:`docker_installation`.
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1. Install the MegaQC package
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-----------------------------
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.. _Python MySQL connector: https://dev.mysql.com/downloads/connector/python/2.1.html
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.. _PyPI package: https://pypi.python.org/pypi/mysql-connector-python/2.0.4
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.. _create an issue: https://github.com/ewels/MegaQC/issues/new
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.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
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.. _create an issue: https://github.com/MultiQC/MegaQC/issues/new
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.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/main/deployment

‎docs/source/docs/troubleshooting.rst

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- When creating a violin plot I get an error.
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- This is a known issue: https://github.com/ewels/MegaQC/issues/31
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- This is a known issue: https://github.com/MultiQC/MegaQC/issues/31
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- TypeError: '<' not supported between instances of 'NoneType' and 'float' when trying to compare data
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- This is a known issue: https://github.com/ewels/MegaQC/issues/156
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- This is a known issue: https://github.com/MultiQC/MegaQC/issues/156
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- Please ensure that your reports do not have missing fields

‎megaqc/templates/footer.html

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<p>
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<a href="http://multiqc.info/db" target="_blank">MegaQC v{{ version }}</a>
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- Written by Phil Ewels, Denis Moreno, Michael Milton, Tor Solli-Nowlan and Lukas Heumos,
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available on <a href="https://github.com/ewels/MegaQC" target="_blank">GitHub</a>.
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available on <a href="https://github.com/MultiQC/MegaQC" target="_blank">GitHub</a>.
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</p>
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<p>
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MegaQC uses

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