- Command Line interface for Linux and Windows
- Single Directory Upload
- Miseq sequencing run parser
- Automated uploads
- File upload checksum validation
- Post-processing tasks
- Pause and resume uploads
Download / Install / Setup
The IRIDA MiSeq Uploader can be run on any operating system that supports Python.
You can download the source code on GitHub.
You can download pre-built packages for Windows from our GitHub releases page.
Run an installer (links above) and follow along with the install wizard.
You will need to configure your uploader before running. See Configuration for details
Make sure Python 3.6 is installed
$ python3.6 --version
If python3 is not installed, install with
$ sudo apt-get install python3.6
$ sudo apt-get install python3-pip
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
Download the source code
$ git clone https://github.com/phac-nml/irida-miseq-uploader $ cd irida-miseq-uploader
Build a virtualenv and install the dependencies automatically with
You will need to configure your uploader before running.
You will need to configure IRIDA and the uploader to upload files.
If you do not create a configuration file, IRIDA uploader will create one for you with default values the first time it try's to upload.
You will need to edit this file with your IRIDA credentials, and the parser that matches your data.
Choose a Parser
The config file has a
parser field that you can use to parse different directory structures
We currently support the following:
directory : Generic Directory
miseq : Miseq
Starting an upload
You can upload with the following commands
Open a Command Prompt terminal and use the
iridauploader command to upload
C:\Users\username> iridauploader \path\to\my\samples\
Use the the
irida-uploader.sh script included with the source code to upload.
Logs are written to your system default logging directory
Check the Errors Page for help with common errors.
Found a bug or have an idea for a feature?
Create an issue on our GitHub Issues Board
Want to create a parser for a sequencer that we don't yet support or have an idea for an IRIDA related project?