{"id":18091305,"url":"https://github.com/jamesetsmith/msanalysis","last_synced_at":"2025-04-13T06:09:06.188Z","repository":{"id":104005780,"uuid":"216615147","full_name":"jamesETsmith/msanalysis","owner":"jamesETsmith","description":"Python Tools for Mass Spec. 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First we suggest installing all of prerequisites in a clean [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) env (run this inside the main directory of the package):\n\n```bash\nconda env create -f devtools/conda-envs/msanalysis_env.yaml\n```\n\nThen install using pip and we're done!\n\n```bash\npython -m pip install -e .\n```\n\nIf you aren't doing this in a conda env and don't have root user privileges use:\n\n```bash\npython -m pip install -e . --user\n```\n\n### Fresh install\n\n```bash\ngit clone https://github.com/jamesETsmith/msanalysis.git\ncd msanalysis\nconda env create -f devtools/conda-envs/msanalysis_env.yaml\npython -m pip install -e .\ncd patches\npython add_elements.py\n```\n\n### Patches\n\nCurrently there is one patch while we wait to hear back on an issue from `PyOpenMS`.\nIf you want to work with species like Indium, run the python script to patch up `msanalysis`.\n\n```bash\ncd patches\npython add_elements.py\n```\n\n---\n## Testing\n\nTo check that everything is working, run the following from the main project directory:\n\n```bash\npytest -v msanalysis --cov=msanalysis\n```\n\n---\n## Copyright\n\nCopyright (c) 2019, James E. T. Smith/ CU Boulder\n\n---\n## Acknowledgements\n \nProject based on the \n[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesetsmith%2Fmsanalysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjamesetsmith%2Fmsanalysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesetsmith%2Fmsanalysis/lists"}