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Install [pipx](https://pipx.pypa.io/stable/installation/)\n - Install poetry using `pipx install poetry`\n - `git clone https://github.com/Knowledge-Graph-Hub/kg-microbe.git`\n - `cd kg-microbe`\n - `poetry install`\n\n## Download resources needed\n - `poetry run kg download` : This will download the resources needed for this project.\n\n## Transform\n - `poetry run kg transform`: This transforms the resources into knowledge graphs (KGs).\n\n##  Merge\n - `poetry run kg merge`: This merges all transformed graphs above.\n\n## Release\n ### Requirements\n In order to be able to make KG releases on this repository, you'll need:\n - Appropriate permissions to this repository.\n - A Github token that has permissions on this repository. [This is how you set it in GitHub](https://docs.github.com/en/organizations/managing-programmatic-access-to-your-organization/setting-a-personal-access-token-policy-for-your-organization#restricting-access-by-personal-access-tokens-classic). Make sure your token has access to this project.\n - Save this token locally assigned to the environemnt variable `GH_TOKEN`\n    ```shell\n    export GH_TOKEN = XXXX\n    ```\n    or add it to your `~/.bash_profile` or `~/.bashrc` file.\n\nIt should be noted that the KG construction process, particularly the transform step  involving trimming of NCBI Taxonomy for any KG and the steps involving the microbial UniProt dataset for KG-Microbe-Function and KG-Microbe-Biomedical-Function, is computationally intensive. Successful execution on a local machine may require significant memory resources (e.g., \u003e500 GB of RAM), further details can be found in the project's code repository.\n\n# Contributors\nPlease remember to run `poetry run tox` before every commit to make sure the code you commit is error-free.\n\n## Environment Variables\nIf you need to use environment variables for this project, copy `.env.example` to `.env` and set the environment variables accordingly:\n```shell\ncp .env.example .env\n```\nThen edit the `.env` file to configure the required environment variables for your setup.\n\n# Acknowledgements\n\nThis [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [kg-cookiecutter](https://github.com/Knowledge-Graph-Hub/kg-cookiecutter) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).\n \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fknowledge-graph-hub%2Fkg-microbe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fknowledge-graph-hub%2Fkg-microbe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fknowledge-graph-hub%2Fkg-microbe/lists"}