{"id":20693461,"url":"https://github.com/nanxstats/sbpack-r","last_synced_at":"2026-04-24T04:33:57.872Z","repository":{"id":142658955,"uuid":"262890984","full_name":"nanxstats/sbpack-r","owner":"nanxstats","description":"An R package to pack and upload CWL apps to Seven Bridges powered platforms","archived":false,"fork":false,"pushed_at":"2020-05-11T06:41:38.000Z","size":50,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-03-25T13:34:10.347Z","etag":null,"topics":["bioinformatics","common-workflow-language","cwl","reticulate"],"latest_commit_sha":null,"homepage":"https://nanx.me/sbpack-r/","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/nanxstats.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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}},"created_at":"2020-05-10T23:01:47.000Z","updated_at":"2020-05-11T06:47:46.000Z","dependencies_parsed_at":null,"dependency_job_id":"df549549-0e8b-423a-969b-decf8392885f","html_url":"https://github.com/nanxstats/sbpack-r","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nanxstats/sbpack-r","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanxstats%2Fsbpack-r","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanxstats%2Fsbpack-r/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanxstats%2Fsbpack-r/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanxstats%2Fsbpack-r/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanxstats","download_url":"https://codeload.github.com/nanxstats/sbpack-r/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanxstats%2Fsbpack-r/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32209893,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-24T03:15:14.334Z","status":"ssl_error","status_checked_at":"2026-04-24T03:15:11.608Z","response_time":64,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["bioinformatics","common-workflow-language","cwl","reticulate"],"created_at":"2024-11-16T23:26:45.942Z","updated_at":"2026-04-24T04:33:57.857Z","avatar_url":"https://github.com/nanxstats.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# sbpack-r\n\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n\nsbpack-r is an R wrapper offering a functional interface for the Python package [sbpack](https://github.com/rabix/sbpack), which supports packing local or remote [Common Workflow Language](https://www.commonwl.org/) (CWL) apps and uploading them to Seven Bridges powered platforms.\n\n## Installation\n\nInstall sbpack-r from GitHub:\n\n```r\nremotes::install_github(\"nanxstats/sbpack-r\")\n```\n\nIt depends on the Python package sbpack. Installed via pip:\n\n```bash\npip3 install git+https://github.com/rabix/sbpack\n```\n\n## Usage\n\n```r\nreticulate::use_python(\"/usr/local/bin/python3\")\nlibrary(\"sbpack\")\n\n\"foo.cwl\" %\u003e% pack_to_file(\"bar.cwl\")\n\"https://example.com/foo.cwl\" %\u003e% pack_to_file(\"bar.cwl\")\n\n\"foo.cwl\" %\u003e% pack_to_sb(\"cgc\", \"user/project/app\")\n\"https://example.com/foo.cwl\" %\u003e% pack_to_sb(\"cgc\", \"user/project/app\")\n```\n\n## Developers\n\nIf you have already installed Python and sbpack, and want to develop sbpack-r in RStudio, simply create a file `.Rprofile` under the package directory and set the Python binary path (Homebrew Python 3 path example below):\n\n```r\nSys.setenv(RETICULATE_PYTHON = \"/usr/local/bin/python3\")\n```\n\nThe next time you open the project, the correct Python path and library path should be already set. For more technical details, see [reticulate Python version configuration](https://rstudio.github.io/reticulate/articles/versions.html).\n\n## Copyright\n\n© 2020 Seven Bridges Genomics, Inc. All rights reserved.\n\nThis project is licensed under the GNU Affero General Public License v3.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanxstats%2Fsbpack-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanxstats%2Fsbpack-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanxstats%2Fsbpack-r/lists"}