Welcome to Mutwil Lab!

Here we maintain tools to study plant biological processes and their evolution through the lens of systems biology.

Please see our wiki for documentation on how to run commonly used pipelines.

Please visit our website for more details

Setup

Clone repository into local machine

$ git clone https://github.com/mutwil/mutwillab.git

Create environment, install required packages

$ cd mutwillab
$ virtualenv -p python .venv
$ source ./.venv/bin/activate
$ pip install --upgrade pip
$ pip install -r ./src/setup/requirements.txt

if the install failed then probably the python version used by virtualenv is not up to date. A quick fix is to install conda and use it to create an environment with python>3.10.

$ conda create --name python_3_10 python=3.10
$ conda activate python_3_10
$ cd mutwillab
$ virtualenv -p python .venv
$ conda deactivate
$ source ./.venv/bin/activate
$ pip install --upgrade pip
$ pip install -r ./src/setup/requirements.txt

That's it! You should have everything you need to import tools into your Python scripts

Importing modules

If using IDEs (like VScode), use this boiler plate at the start of your scripts.

#Boiler plate
import sys
sys.path.insert(0, "/path/to/mutwillab/src/")
sys.path.insert(0, "/path/to/mutwillab/.venv/lib/python3.11/site-packages/")

#Import modules from mutwillab
from coexpression import pearson

#your code

For Mutwil Lab members: If writing executable script for your pipline in main/ folder, your can use this boiler plate.

#Boiler plate
import sys
if __name__ == "__main__":
         abspath= __file__
         parent_module= "/".join(abspath.split("/")[:-2])
         sys.path.insert(0, parent_module)
#Import modules from mutwillab
from coexpression import pearson

Activate virtual enviroment and run the script from CLI.

$ source ./venv/bin/activate
$ python ./src/main/yourscript.py

Happy coding!

ATTENTION

This page is still being worked on. Please be patient with us. More will be revealed. :)