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Repository cloning and initialization

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/repository-cloning-and-initialization

Use when you have a GitHub repository URL, a documented Python version requirement, and a list of pinned package versions, and you need to verify that the application will initialize without import or runtime errors before proceeding to data analysis or method replication.From its SKILL.md

Install
npx -y skills add HolobiomicsLab/asb-skill-collections --skill repository-cloning-and-initialization

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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SKILL.md

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repository-cloning-and-initialization

Summary

Clone a scientific software repository and install its pinned dependencies in an isolated Python environment to verify the documented entrypoint is executable. This skill establishes a reproducible runtime for metabolomics analysis tools (or similar bioinformatics software) before conducting analysis.

When to use

You have a GitHub repository URL, a documented Python version requirement, and a list of pinned package versions, and you need to verify that the application will initialize without import or runtime errors before proceeding to data analysis or method replication.

When NOT to use

  • The repository documentation does not specify pinned dependency versions (use a requirements file discovery step first).
  • The application has no documented entrypoint or README with setup instructions.
  • You already have a pre-configured containerized or conda environment and do not need to verify manual installation.

Inputs

  • GitHub repository URL
  • Python version requirement (e.g., >=3.9)
  • Pinned dependency list with exact version numbers

Outputs

  • Activated Python virtual environment with all dependencies installed
  • Successful entrypoint invocation confirmation (no import or runtime errors)
  • Initialized application instance ready for analysis

How to apply

Clone the repository from the documented GitHub URL (e.g., github.com/Leo-Cheng-Lab/ROIAL-NMR). Create a new Python virtual environment with the required Python version (≥3.9 for ROIAL-NMR) to isolate dependencies. Install each pinned dependency using pip with exact version numbers (e.g., XlsxWriter==3.2.2, pandas==2.2.3, PyQt5==5.15.11, openpyxl==3.1.5). Execute the documented entrypoint command (e.g., python main.py) to confirm the application initializes, all imports resolve, and no runtime errors occur. Record success as confirmation that the environment is correctly configured and the tool is ready for use.

Related tools

  • Python (Runtime interpreter and environment manager for dependency installation and entrypoint execution) — https://www.anaconda.com/download/
  • XlsxWriter (Excel file output generation for metabolite analysis results)
  • pandas (Data manipulation and tabular data handling for metabolite identification results)
  • PyQt5 (GUI framework for ROIAL-NMR interactive analysis interface)
  • openpyxl (Excel file reading and writing for parameter input and result export)

Examples

git clone https://github.com/Leo-Cheng-Lab/ROIAL-NMR && cd ROIAL-NMR && python -m venv env && source env/bin/activate && pip install XlsxWriter==3.2.2 pandas==2.2.3 PyQt5==5.15.11 openpyxl==3.1.5 && python main.py

Evaluation signals

  • Virtual environment successfully created and activated with the specified Python version.
  • All pinned dependencies install without version conflicts or deprecation warnings.
  • Entrypoint command (python main.py) executes without ImportError, ModuleNotFoundError, or AttributeError.
  • Application initializes to a usable state (GUI window displays, or CLI prompt appears, with no stderr tracebacks).
  • No runtime errors occur during the first interaction with the application (e.g., opening the default analysis template or viewing the main window).

Limitations

  • This skill verifies only that the documented environment can be instantiated; it does not validate that analysis results are correct or that the tool functions correctly on real data.
  • Platform-specific issues (e.g., PyQt5 on headless servers, macOS vs. Linux linker differences) may cause entrypoint failures despite correct dependency versions.
  • No changelog is provided in the repository, so it is not possible to trace which dependency versions correspond to which feature set or bug fixes.
  • Pinned dependency versions may become outdated or unavailable on PyPI, requiring alternative versions or manual source builds.

Evidence

  • [other] ROIAL-NMR requires Python >=3.9 and five pinned dependencies (XlsxWriter 3.2.2, pandas 2.2.3, PyQt5 5.15.11, openpyxl 3.1.5): "ROIAL-NMR requires Python >=3.9 and five pinned dependencies (XlsxWriter 3.2.2, pandas 2.2.3, PyQt5 5.15.11, openpyxl 3.1.5) to be installed"
  • [other] Clone the ROIAL-NMR repository from github.com/Leo-Cheng-Lab/ROIAL-NMR. Create a Python virtual environment with Python ≥3.9.: "Clone the ROIAL-NMR repository from github.com/Leo-Cheng-Lab/ROIAL-NMR. 2. Create a Python virtual environment with Python ≥3.9."
  • [other] Install dependencies using pip with exact versions and Execute python main.py to confirm the entrypoint is invokable and the application initializes without import or runtime errors.: "Install dependencies using pip with exact versions: XlsxWriter 3.2.2, pandas 2.2.3, PyQt5 5.15.11, and openpyxl 3.1.5. 4. Execute python main.py to confirm the entrypoint is invokable and the"
  • [readme] Python version and packages requirements with exact pinned versions: "1. Python>=3.9
  1. XlsxWriter 3.2.2
  2. pandas 2.2.3
  3. PyQt5 5.15.11
  4. openpyxl 3.1.5"

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