iridauploader 0.6.0

IRIDA uploader: upload NGS data to IRIDA system

IRIDA Uploader

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

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 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>

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 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