ofp-sam-CondorBox

CondorBox packages your GitHub repository into a Docker container and submits it to an HTCondor cluster for reproducible, scalable high-performance computing.

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Overview

The CondorBox package provides the following functionalities:

1. Clone and Run a GitHub Repository on HTCondor:

   • Use the CondorBox() function to package a GitHub repository into a Docker container, submit it to an HTCondor cluster, and execute the desired operations remotely.

2. Sync Results Locally:

   • After the job completes remotely, use the CondorUnbox() function to download the results from the remote server, extract the output, and synchronise it with your local project directory.

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Dependencies

General Requirements

To use CondorBox, ensure the following dependencies are installed and configured on your system:

1. Docker

   • Docker is required to build and run containers.
   • Install Docker from https://www.docker.com/products/docker-desktop.
   • On Windows, ensure Docker Desktop is running.

2. GNU Make

   • Make is required for automating tasks defined in Makefiles.

   • For Windows users, make can be installed via:

     • Rtools (Recommended for R users):
       Download from https://cran.r-project.org/bin/windows/Rtools/.
     • MinGW or Chocolatey:
       Use these package managers to install make.

   • For Linux users:

     sudo apt-get install build-essential

   • For macOS users:

     xcode-select --install

3. Git Bash (for Windows)

   • Required to execute UNIX-style shell commands on Windows.
   • Install Git from https://git-scm.com/downloads.

4. SSH Access

   • SSH should be set up for secure communication with the remote server.
   • Test connectivity:

     ssh [email protected]

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GitHub Personal Access Token (PAT)

To access private GitHub repositories or to authenticate securely, you need a GitHub Personal Access Token (PAT).

Steps to Obtain a GitHub PAT

1. Log in to your GitHub account at https://github.com/.

2. Navigate to Settings > Developer settings > Personal access tokens > Tokens (classic).

3. Click Generate new token > Generate new token (classic).

4. Provide a descriptive note (e.g., "CondorBox access").

5. Set the expiration date for the token (e.g., 30 days).

6. Select the following scopes:

   • repo (Full control of private repositories)
   • read:org (Optional: Access organisational resources)

7. Click Generate token.

8. Copy the generated token immediately and store it securely. (It will not be shown again.)

Using the GitHub PAT with CondorBox

• Save your GitHub PAT as an environment variable to avoid hardcoding it into scripts:

  Sys.setenv(GitPass = "your_github_pat")

• Use the Sys.getenv("GitPass") function to access the GitHub PAT in your scripts.