IRIDA uploader: upload NGS data to IRIDA system
Project description
IRIDA Uploader
Download / Installation
The IRIDA Uploader is available via pip
and bioconda
Installation instructions can be found in our documentation.
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
Test Coverage
You can run the entire test suite and generate a coverage report with the following command:
$ make coverage
To view the detailed report, open the generated htmlcov/index.html
with your web browser.
Documentation
You can ReadTheDocs 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
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