{"id":19624044,"url":"https://github.com/bioconductor/basilisk","last_synced_at":"2025-04-28T05:31:07.730Z","repository":{"id":39311566,"uuid":"150755578","full_name":"Bioconductor/basilisk","owner":"Bioconductor","description":"Clone of the Bioconductor repository for the basilisk package.","archived":false,"fork":false,"pushed_at":"2024-07-27T07:23:20.000Z","size":509,"stargazers_count":27,"open_issues_count":10,"forks_count":14,"subscribers_count":8,"default_branch":"master","last_synced_at":"2024-09-10T11:12:15.750Z","etag":null,"topics":["bioconductor-package"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/devel/bioc/html/basilisk.html","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2018-09-28T14:51:32.000Z","updated_at":"2024-07-27T07:23:22.000Z","dependencies_parsed_at":"2024-02-17T22:23:28.228Z","dependency_job_id":"de08104e-d1bd-4700-8bcf-65d9e245f141","html_url":"https://github.com/Bioconductor/basilisk","commit_stats":{"total_commits":463,"total_committers":11,"mean_commits":42.09090909090909,"dds":"0.056155507559395246","last_synced_commit":"8014ad72609686233ac7bbe0cb5a2eb8ac302fe8"},"previous_names":["bioconductor/basilisk"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbasilisk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbasilisk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbasilisk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbasilisk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/basilisk/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096711,"owners_count":17255146,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["bioconductor-package"],"created_at":"2024-11-11T11:36:40.087Z","updated_at":"2025-04-28T05:31:07.710Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Managing Python environments within Bioconductor\n\n|Environment|Status|\n|---|---|\n|BioC-release|[![Release OK](https://bioconductor.org/shields/build/release/bioc/basilisk.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/basilisk/)|\n|BioC-devel|[![Devel OK](https://bioconductor.org/shields/build/devel/bioc/basilisk.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/basilisk/)|\n\n**basilisk** provides a standardized mechanism for handling Python dependencies within Bioconductor packages.\nIt does so by automatically provisioning and managing one or more Conda environments per BioC package,\nensuring that the end-user is not burdened with the responsibility of meeting any Python-based `SystemRequirements`.\nWe integrate with **reticulate** to allow intuitive calling of Python code within R,\nwith additional protection to ensure that multiple Python environments can be called within the same R session.\n\nMost \"users\" of this package are expected to be Bioconductor package developers;\nend users should not need to interact with the **basilisk** machinery, all going well.\nUsers can follow the typical installation process for Bioconductor packages:\n\n```r\ninstall.packages(\"BiocManager\") # if not already installed\nBiocManager::install(\"basilisk\")\n\n# Bioconductor package developers may prefer to use the devel version:\nBiocManager::install(\"basilisk\", version=\"devel\") \n```\n\nThe [vignette](https://bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html) provides instructions on how to adapt a client package to use **basilisk**.\nA minimal example is provided in the [`inst/example`](inst/example/) directory and contains code like:\n\n```r\n# Provision an environment.\nmy_env \u003c- BasiliskEnvironment(envname=\"my_env_name\",\n    pkgname=\"name.of.package\",\n    packages=c(\"pandas==0.25.1\")\n)\n\n# Run reticulate code using that environment.\nres \u003c- basiliskRun(env=my_env, fun=function(args) {\n    out \u003c- reticulate::import(\"pandas\")\n    # Do something with pandas\n    return(some_r_object)\n})\n```\n\nDetailed documentation for each function is available through the usual methods, i.e., `?basiliskRun`.\nSee the [Bioconductor landing page](https://bioconductor.org/packages/basilisk) for more links;\nsome examples of **basilisk** client packages include [**crisprScore**](https://bioconductor.org/packages/crisprScore) and [**velociraptor**](https://bioconductor.org/packages/velociraptor).\n\nBugs can be posted to the [Issues](https://github.com/LTLA/basilisk/issues) of this repository.\nPull requests are welcome.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbasilisk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbasilisk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbasilisk/lists"}