Synthedia can be downloaded and installed locally. This is recommended if you're trying to produce large numbers of mzML files or require a quicker output. Installation instructions are below. Alternatively, the source code can be found here.
Install via pip
Create a virtual environment (optional):
virtualenv venv
source venv/bin/activate
pip install --upgrade pip
Note that the pyOpenMS dependency of synthedia requires python 3.7, 3.8 or 3.9. If you have multiple python versions installed, you can construct virtual environments with different versions by:
virtualenv venv --python=/path/to/python3.X
On linux systems, the path is usually /usr/bin/pythonX.X
Install synthedia using pip
pip install synthedia
Install from source
Clone the repo:
git clone https://github.com/mgleeming/synthedia.git
cd synthedia
Create a virtual environment (optional):
virtualenv venv
source venv/bin/activate
pip install --upgrade pip
Note that the pyOpenMS dependency of synthedia requires python 3.7, 3.8 or 3.9. If you have multiple python versions installed, you can construct virtual environments with different versions by:
virtualenv venv --python=/path/to/python3.X
On linux systems, the path is usually /usr/bin/pythonX.X
Install dependencies
pip install -r requirements.txt
Install synthedia:
pip install .
Synthedia can then be invoked from the command line by:
synthedia [COMMAND LINE ARGUMENTS]
Optionally, you can run the Synthedia integration test to check that everything is working:
pip install pytest
pytest -v
