{"id":27172097,"url":"https://github.com/pacificcommunity/ofp-sam-condorbox","last_synced_at":"2026-04-26T12:31:20.630Z","repository":{"id":273663700,"uuid":"919194249","full_name":"PacificCommunity/ofp-sam-CondorBox","owner":"PacificCommunity","description":"CondorBox packages your GitHub repository into a Docker container and submits it to an HTCondor cluster for reproducible, scalable high-performance computing.","archived":false,"fork":false,"pushed_at":"2025-07-14T04:42:37.000Z","size":212,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-07-14T09:01:52.306Z","etag":null,"topics":["docker","htcondor","ofp","sam"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PacificCommunity.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-01-19T23:30:34.000Z","updated_at":"2025-07-14T04:42:40.000Z","dependencies_parsed_at":"2025-04-09T09:46:56.742Z","dependency_job_id":null,"html_url":"https://github.com/PacificCommunity/ofp-sam-CondorBox","commit_stats":null,"previous_names":["pacificcommunity/ofp-sam-condorbox"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/PacificCommunity/ofp-sam-CondorBox","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-CondorBox","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-CondorBox/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-CondorBox/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-CondorBox/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PacificCommunity","download_url":"https://codeload.github.com/PacificCommunity/ofp-sam-CondorBox/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-CondorBox/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32297893,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-26T09:34:17.070Z","status":"ssl_error","status_checked_at":"2026-04-26T09:34:00.993Z","response_time":129,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["docker","htcondor","ofp","sam"],"created_at":"2025-04-09T09:35:12.303Z","updated_at":"2026-04-26T12:31:20.612Z","avatar_url":"https://github.com/PacificCommunity.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ofp-sam-CondorBox\n\n**CondorBox** packages your GitHub repository into a Docker container and submits it to an HTCondor cluster for reproducible, scalable high-performance computing.\n\n---\n\n## Overview\n\nThe **CondorBox** package provides the following functionalities:\n\n1. **Clone and Run a GitHub Repository on HTCondor:**\n   - 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.\n   \n2. **Sync Results Locally:**\n   - 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.\n\n---\n\n## Dependencies\n\n### General Requirements\n\nTo use **CondorBox**, ensure the following dependencies are installed and configured on your system:\n\n1. **Docker**  \n   - Docker is required to build and run containers.  \n   - Install Docker from [https://www.docker.com/products/docker-desktop](https://www.docker.com/products/docker-desktop).  \n   - On Windows, ensure **Docker Desktop** is running.\n\n2. **GNU Make**  \n   - Make is required for automating tasks defined in Makefiles.  \n   - For **Windows** users, `make` can be installed via:\n     - **Rtools** (Recommended for R users):  \n       Download from [https://cran.r-project.org/bin/windows/Rtools/](https://cran.r-project.org/bin/windows/Rtools/).\n     - **MinGW** or **Chocolatey**:  \n       Use these package managers to install `make`.\n\n   - For **Linux** users:  \n     ```bash\n     sudo apt-get install build-essential\n     ```\n\n   - For **macOS** users:  \n     ```bash\n     xcode-select --install\n     ```\n\n3. **Git Bash (for Windows)**  \n   - Required to execute UNIX-style shell commands on Windows.  \n   - Install Git from [https://git-scm.com/downloads](https://git-scm.com/downloads).\n\n4. **SSH Access**  \n   - SSH should be set up for secure communication with the remote server.  \n   - Test connectivity:  \n     ```bash\n     ssh your_username@remote.server.com\n     ```\n\n---\n\n## GitHub Personal Access Token (PAT)\n\nTo access private GitHub repositories or to authenticate securely, you need a **GitHub Personal Access Token (PAT)**.\n\n### Steps to Obtain a GitHub PAT\n\n1. Log in to your GitHub account at [https://github.com/](https://github.com/).\n\n2. Navigate to **Settings** \u003e **Developer settings** \u003e **Personal access tokens** \u003e **Tokens (classic)**.\n\n3. Click **Generate new token** \u003e **Generate new token (classic)**.\n\n4. Provide a descriptive **note** (e.g., \"CondorBox access\").\n\n5. Set the **expiration** date for the token (e.g., 30 days).\n\n6. Select the following **scopes**:\n   - `repo` (Full control of private repositories)\n   - `read:org` (Optional: Access organisational resources)\n\n7. Click **Generate token**.\n\n8. Copy the generated token **immediately** and store it securely. (It will not be shown again.)\n\n### Using the GitHub PAT with CondorBox\n\n- Save your GitHub PAT as an environment variable to avoid hardcoding it into scripts:\n  ```r\n  Sys.setenv(GitPass = \"your_github_pat\")\n  ```\n- Use the `Sys.getenv(\"GitPass\")` function to access the GitHub PAT in your scripts.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpacificcommunity%2Fofp-sam-condorbox","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpacificcommunity%2Fofp-sam-condorbox","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpacificcommunity%2Fofp-sam-condorbox/lists"}