This page includes information about the underlying scripts of Metaboverse and Metaboverse-cli and how to contribute to and modify the software.
Once you have made the desired changes, you can submit a Pull Request, which will be reviewed and incorporated into the code base for future deployment if the changes meet the required standards. You should reference the documentation: https://docs.github.com/en/pull-requests.
metaboverse-clihandles a large portion of the backend processing, primarily to curate the metabolic network for the organism of interest and to layer the user’s data onto said network. The source code is generally organized as follows:
metaboverse-cli ├── setup.py: The command line tool setup file ├── requirements.txt: The depencency file used for distribution ├── metaboverse-cli.spec: The Pyinstaller file to compile the distributable executable └── /metaboverse_cli ├── arguments.py: A file to set and parse user-provided command line arguments ├── __main__.py: The main execution script for the backend ├── /mapper: This submodule generates the metabolite synonym mapper that assists │ in mapping user data to the metabolic network ├── /curate: This submodule builds the organism specific reaction network and │ stores any relevant metadata about the reaction network component └── /analyze: This submodule handles layering the user's data onto the metabolic network. This includes implementing the metabolite synonym mappper. This submodule also handles generating the reaction network with reaction collapsing
Metaboversehandles the front-end user interface and data visualization, and performed reaction pattern recognition in real-time. The source code is generally organized as follows:
Documentation and Testing¶
$ conda create --name pyinstaller $ conda activate pyinstaller $ conda config --add channels conda-forge $ conda install python=3.8
$ conda install pyinstaller $ conda install --file requirements.txt
$ pip install pyinstaller $ pip install -r requirements.txt
$ cd /path-to/metaboverse-cli $ pyinstaller metaboverse-cli.spec
metaboverse-cliexecutables for each operating system. These should be stored in the directory,
$ cd /path-to/Metaboverse $ bash build.sh
You will likely need to compile the Metaboverse package for Mac on a Mac. If the Mac-version
metaboverse-cli executable is packaged into Metaboverse via Electron on another operating system, we have consistently received an error in executing