Metadata-Version: 2.1
Name: iridauploader
Version: 0.8.2
Summary: IRIDA uploader: upload NGS data to IRIDA system
Home-page: https://github.com/phac-nml/irida-uploader
Author: Jeffrey Thiessen
Author-email: jeffrey.thiessen@canada.ca
License: Apache-2.0
Description: IRIDA Uploader
        ==============
        
        [![Integration Tests](https://github.com/phac-nml/irida-uploader/workflows/Integration%20Tests/badge.svg?branch=development&event=schedule)](https://github.com/phac-nml/irida-uploader/actions?query=branch%3Adevelopment)
        [![Documentation Status](https://readthedocs.org/projects/irida-uploader/badge/?version=stable)](https://irida-uploader.readthedocs.io/en/stable/?badge=stable)
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/irida-uploader/README.html)
        
        **Please Note: The latest version of the IRIDA Uploader requires IRIDA Version 20.05 or later.**
        
        If you are using an older version of IRIDA, please update your IRIDA, or use Uploader Release Version 0.4.3
        
        Download / Installation
        --------------------
        
        The IRIDA Uploader is available via `pip` and `bioconda`
        
        Installation instructions can be found in our documentation.
        
        [ReadTheDocs](https://irida-uploader.readthedocs.io/en/stable/)
        
        Tutorial
        --------
        
        You can find a walkthrough and tutorial on the phac-nml github
        
        https://github.com/phac-nml/irida-uploader-tutorial
        
        Running the project from source code
        --------------------------
        You can build an environment and run the uploader from source code with the following commands:
        
            $ make
            $ source .virtualenv/bin/activate
            $ irida-uploader --help
        
        You can also build and run the GUI with:
        
            $ make gui
            $ source .virtualenv/bin/activate
            $ irida-uploader-gui
        
        Creating the Windows installer from source code
        ------------------------------
        
        A new windows installer can be built on linux, so first see the installation instructions for installing on linux in our documentation.
        
        You will also need `nsis` installed to create the windows installer.
        
            $ sudo apt install nsis
        
        Then run the command:
        
            $ make windows
            
        This will create a new installer in the folder `build/nsis/` with a name similar to `IRIDA_Uploader_GUI_0.X.X.exe`
        
        Running Tests
        -------------
        
        #### Unit tests
        
        Running the unittests can be done with the command:
        
            $ make unittests
        
        #### Integration tests
        
        To run integration tests You will need to download and install chromedriver http://chromedriver.chromium.org/downloads
        
        You will need to grant the IRIDA instance access to the mysql database needed for the tests
        
            $ mysql -e "CREATE USER 'test'@'localhost' IDENTIFIED BY 'test'; GRANT ALL ON irida_uploader_test.* to 'test'@'localhost';"
        
        Running the IRIDA integration tests can be done with the command:
        
            $ make integrationtests branch=<IRIDA github branch to test against>
        
        Example:
        
            $ make integrationtests branch=development
        
        Tests will be logged to `~/.cache/irida_uploader_test/log/irida-uploader.log`
        
        #### PEP8 tests
        
        You can run pep8 tests with:
        
            $ make pep8
        
        Documentation
        ------------------------------
        You can [ReadTheDocs](https://irida-uploader.readthedocs.io/en/stable/) here.
        
        Alternatively, documentation is built locally using `mkdocs`. 
        
        It can be built with the command:
        
            $ make docs
        
        Or you can install mkdocs to your system:
        
            $ sudo apt install mkdocs
            $ mkdocs build
        
        HTML docs will be generated to `site/` for local browsing
        
Keywords: IRIDA NGS uploader
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: GUI
Provides-Extra: TEST
Provides-Extra: WINDOWS
