Repository Cloning And Setup

---
name: repository-cloning-and-setup
description: Use when when you need to deploy a containerized scientific tool (e.g.,
  CloMet) for the first time on a local machine or CI/CD environment, and the project
  provides a Dockerfile and GitHub repository.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3778
  edam_topics:
  - http://edamontology.org/topic_3407
  tools:
  - Docker
  - Git
  - CloMet
  techniques:
  - NMR
  license_tier: open
  provenance_tier: literature
derived_from:
- doi: 10.1021/acs.jproteome.2c00602
  title: CloMet
evidence_spans: []
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_clomet_cq
    doi: 10.1021/acs.jproteome.2c00602
    title: CloMet
  dedup_kept_from: coll_clomet_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/acs.jproteome.2c00602
  all_source_dois:
  - 10.1021/acs.jproteome.2c00602
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# repository-cloning-and-setup

## Summary

Clone a GitHub repository and prepare its Docker environment for first-time execution. This skill establishes a reproducible, containerized runtime for tools like CloMet that harmonize NMR-based metabolomics data across public repositories.

## When to use

When you need to deploy a containerized scientific tool (e.g., CloMet) for the first time on a local machine or CI/CD environment, and the project provides a Dockerfile and GitHub repository. Specifically: (1) you have Docker installed on your target OS, (2) you need to access the tool's source code and build configuration, and (3) you want to verify the tool initializes and responds to basic commands (e.g., help, version) before use.

## When NOT to use

- The tool is already installed and running natively on your system without Docker containerization.
- Docker is not available or cannot be installed on your target platform.
- You only need to download source code for inspection and do not intend to build or execute the containerized tool.

## Inputs

- GitHub repository URL (e.g., github:rmallol__clomet)
- Operating system identifier (for Docker installation selection)
- Dockerfile (in repository root)

## Outputs

- Local clone of the repository (directory tree with source code and Dockerfile)
- Built Docker image with CloMet environment and dependencies
- Running Docker container instance
- Tool initialization response (e.g., help text or version string)

## How to apply

First, install Docker following the official procedure for your operating system. Second, clone the CloMet repository from the GitHub remote (github:rmallol__clomet) using standard git clone. Third, navigate to the repository root and build the Docker image from the provided Dockerfile, which encapsulates all CloMet dependencies and configuration. Fourth, run the resulting container with appropriate volume mounts to expose data directories and verify it starts without errors. Fifth, execute an initial validation command (e.g., help or version check) inside the container to confirm the tool is functional and accessible. Success is indicated by clean container startup and a successful tool invocation response.

## Related tools

- **Docker** (Containerization engine to build and run CloMet in an isolated, reproducible environment with all declared dependencies.)
- **Git** (Version control system to clone the CloMet repository from GitHub.)
- **CloMet** (NMR-based metabolomics data harmonization tool; the target application being set up.) — https://github.com/rmallol/clomet

## Evaluation signals

- Docker image builds without compilation errors or missing dependencies; `docker build -t clomet .` completes successfully.
- Container starts without immediate exit or runtime errors; `docker run clomet` does not throw exceptions on entry.
- Tool responds to initialization commands; `docker run clomet help` or `docker run clomet --version` returns expected output.
- Volume mounts are correctly configured; data in mounted directories is accessible and readable from inside the container.
- Repository files (source code, Dockerfile, configuration) are present and intact in the cloned local directory.

## Limitations

- Requires Docker to be pre-installed and properly configured on the host system; installation procedure varies by OS and may require administrative privileges.
- Network connectivity is required to clone the repository from GitHub; firewall or proxy restrictions may block git clone.
- No changelog is documented in the repository, so version history and breaking changes between releases are not readily available.
- The setup procedure assumes a Linux/Unix-like environment inside the container; host OS compatibility depends on Docker's runtime support.

## Evidence

- [intro] First-time Docker installation and CloMet execution: "Follow these steps to install Docker and run CloMet for the first time"
- [other] Multi-step workflow includes repository cloning and Docker image build: "Clone the CloMet repository from github:rmallol__clomet. 3. Build the CloMet Docker image from the provided Dockerfile"
- [other] Verification via container execution and tool invocation: "Run the CloMet container with appropriate volume mounts and verify that the containerized tool starts without errors. 5. Execute an initial CloMet command (e.g., help or version check) to confirm the"
- [readme] CloMet's core function and modular design: "CloMet eases the connection between public data repositories and data analysis platforms by harmonizing the file systems of available data sets, with a focus on NMR-based metabolomics"
- [readme] Modularity supports extension and community contribution: "The software has been designed in such a modular way meeting the Object Oriented Programming standards to facilitate the extension of its capabilities"