IRIDA Uploader

NOTICE!

This repo will be deprecated as of January 1st 2020, as Python 2 will be End of Life.

Please use our new uploader https://github.com/phac-nml/irida-uploader

Windows Installation

Download the installer from https://github.com/phac-nml/irida-miseq-uploader/releases

Running in Linux

Install pip and wxpython:

$ sudo apt-get install python-pip python-wxgtk3.0

virtualenv usage

Install virtualenv and setuptools

$ pip install virtualenv
$ pip install setuptools

If you already have these packages installed, ensure they are up to date

$ pip install virtualenv -U
$ pip install setuptools -U

Build a virtualenv and install the dependencies:

$ git clone https://github.com/phac-nml/irida-miseq-uploader
$ cd irida-miseq-uploader
$ make requirements
$ source .virtualenv/bin/activate

You can then run the uploader by running:

$ ./run_IRIDA_Uploader.py

Deactivate when finished:

$ deactivate

Creating the Windows installer

Requirements

You must install several packages to build the Windows installer:

sudo apt-get install innoextract nsis python-pip python-virtualenv

Building the Windows installer

From inside the irida-miseq-uploader directory, you can simply run:

make windows

This will build a Windows installer inside the build/nsis/ directory, named something like IRIDA_Uploader_1.0.0.exe.

Running Tests

You can run all tests (unit and integration) by running:

$ echo "grant all privileges on irida_uploader_test.* to 'test'@'localhost' identified by 'test';" | mysql -u mysql_user -p
$ make test

You can verify PEP8 conformity by running:

$ ./scripts/verifyPEP8.sh

Note: No output is produced (other than pip-related output) if the PEP8 verification succeeds.