IRIDA Uploader
Features
- Command Line interface for Linux and Windows
- Single Directory Upload
- Miseq sequencing run parser
Upcoming Features
- Automated uploads
- File upload checksum validation
- Post-processing tasks
- GUI
- Pause and resume uploads
Getting Started
Download / Install / Setup
Download
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.
Installation
Windows
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
Linux
Make sure Python 3.6 is installed
$ python3.6 --version
If python3 is not installed, install with
$ sudo apt-get install python3.6
Install pip:
$ sudo apt-get install python3-pip
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
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 make
:
$ make
You will need to configure your uploader before running.
Configuration
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
Windows:
Open a Command Prompt terminal and use the iridauploader
command to upload
C:\Users\username> iridauploader \path\to\my\samples\
Linux:
Use the the irida-uploader.sh
script included with the source code to upload.
./irida-uploader.sh /path/to/the/sequencing/run/
Logging
Logs are written to your system default logging directory
Linux
/home/<user>/.cache/irida_uploader/log/
Windows
C:\Users\<username>\AppData\Local\irida_uploader\irida_uploader\Logs
Problems?
Problems uploading?
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
Developers
Want to create a parser for a sequencer that we don't yet support or have an idea for an IRIDA related project?