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IRIDA uploader: upload NGS data to IRIDA system

Project description

IRIDA Uploader

Build Status Documentation Status install with bioconda

Download / Installation

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

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_1.0.exe

Running Tests

Unit tests

Running the unittests can be done with the command:

$ make unittests

IRIDA Integration

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

Tests will be logged to ~/.cache/irida_uploader_test/log/irida-uploader.log

PEP8

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

Project details


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