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https://github.com/btraven00/clustbench-analysis

https://github.com/btraven00/clustbench-analysis

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (9.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: btraven00
  • Language: Python
  • Default Branch: main
  • Size: 103 KB
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  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
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Created about 1 year ago · Last pushed 12 months ago
Metadata Files
Readme

README.docker.md

Docker Setup for Clustbench Analysis

This project uses Nix to create a reproducible Docker environment for R and Python analysis tasks.

Quick Start

Build and load the Docker image:

```bash

Build everything with the helper script

./rebuild_docker.sh

Or manually:

nix-build docker.nix -A image docker load < result nix-build docker.nix -A run ```

Run the Docker container with your current directory mounted:

bash ./result/bin/run-clustbench-docker

This gives you a shell with: - R with all required packages (tidyverse, patchwork, etc.) - Python 3.12 with pandas and numpy

Running Specific Commands

Run R inside the container:

bash ./result/bin/run-clustbench-docker R

Run an R script:

bash ./result/bin/run-clustbench-docker Rscript your_script.R

Run a Python script:

bash ./result/bin/run-clustbench-docker python your_script.py

Troubleshooting

If you get missing R package errors:

Verify your R package dependencies:

bash ./result/bin/run-clustbench-docker Rscript verify_docker_deps.R

To fix dependency issues: 1. Add the missing packages to nix/default.nix in the rPackageList 2. Add critical dependencies (e.g., xfun for knitr) to essentialRDeps in docker.nix 3. Rebuild the Docker image with ./rebuild_docker.sh

If you get a networking error:

The helper script already uses --network=none to avoid common Docker networking issues. Use --network=host as the first argument to enable network access:

bash ./result/bin/run-clustbench-docker --network=host R

If you get permission errors:

Make sure your current directory is readable/writable by the container:

bash chmod -R 755 .

Image Architecture

  • The Docker container uses rWrapper to include R with all dependencies
  • Essential packages and their dependencies are explicitly included
  • R environment is configured via a custom .Rprofile
  • The container works offline by default for reproducibility
  • All data processing happens in mounted directories for persistence

Owner

  • Name: btraven
  • Login: btraven00
  • Kind: user

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