mytardis-mydata-parser

mytardis-mydata-parser filters and parses Illumina MiSeq run results and uploads them to MyTardis via mydata-python and moves parsed and original files to desired backup location.

Dependencies

• mydata-python
• Python>=3.6

1. Create a virtual environment
2. Python dependencies are installed to your venv from requirements.txt: pip install -r requirements.txt

Install mydata-python

Linux:

3. Clone MyData-Python: git clone https://github.com/mytardis/mydata-python.git
4. cd mydata-python
5. python setup.py install
6. Use mydata config generate to setup a config file with your MyTardis API key and username
7. Install and setup rclone (instructions: https://blog.spatialmsk.com/cloud-storage-sync/)
8. Add environmental variables from configs/mytd_api_configs.env.txt to bashrc:

# enter VIM text editor for bashrc
sudo vim ~/.profile

# Update with your username and password and paste into the bottom of profile
export MYTARDIS_API_USER=your_mytardis_username
export MYTARDIS_API_PASSWORD=your_mytardis_password
# save and exit VIM
:wq!

Normally we would use ~/.bashrc, but since we are running a non-interactive shell, bashrc will not source. To avoid this issue, the environmental variables are set in ~/.profile and sourced from within rclone-cron.sh.

Use python run.py [command] to run from Windows. Necessary to get around FileNotFoundError: [WinError 2] The system cannot find the file specified. Files missing from python setup.py install for Windows. To uninstall, run pip uninstall mydata-python.