IRIDA uploader: upload NGS data to IRIDA system
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
Installation instructions can be found in our documentation.
You can find a walkthrough and tutorial on the phac-nml github
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
Running the unittests can be done with the command:
$ make unittests
To run integration tests your will need some additional software.
$ sudo apt install xvfb
You will also 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>
$ make integrationtests branch=development
Tests will be logged to
You can run pep8 tests with:
$ make pep8
You can ReadTheDocs here.
Alternatively, documentation is built locally using
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
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