{"id":19624234,"url":"https://github.com/bioconductor/biocgithubhelp","last_synced_at":"2026-03-09T03:30:55.146Z","repository":{"id":4878876,"uuid":"6034125","full_name":"Bioconductor/BiocGithubHelp","owner":"Bioconductor","description":"Notes and tips for using github with Biocondcutor","archived":false,"fork":false,"pushed_at":"2023-03-15T20:24:35.000Z","size":7,"stargazers_count":7,"open_issues_count":0,"forks_count":4,"subscribers_count":18,"default_branch":"devel","last_synced_at":"2025-01-09T11:58:12.448Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"richharms/ChuckNorrisiOS","license":null,"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":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2012-10-01T18:25:28.000Z","updated_at":"2023-03-15T20:24:39.000Z","dependencies_parsed_at":"2023-07-05T20:32:10.235Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/BiocGithubHelp","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocGithubHelp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocGithubHelp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocGithubHelp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocGithubHelp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/BiocGithubHelp/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240923037,"owners_count":19879238,"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":[],"created_at":"2024-11-11T11:37:22.255Z","updated_at":"2026-03-09T03:30:55.063Z","avatar_url":"https://github.com/Bioconductor.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"## See the \u003ca href=\"https://github.com/Bioconductor/BiocGithubHelp/wiki/\"\u003ewiki\u003c/a\u003e for notes and tips for using github with Biocondcutor\n\u003c!--\nEvery bioc/fhcrc project (including this one, the githubCribsheet) is a separate repository maintained under \n\n   https://github.com/Bioconductor\n   \n### Create your own project (aka repository, or 'repo'):\n\n * Register as a user:  https://github.com/signup/free\n * Send an email to pshannon AT fhcrc.org so that I can give you permissions to create your repo under Bioconductor.\n * Go to https://github.com/Bioconductor.  Sign in.\n * Create your new repo by clicking on the leftmost of the three buttons you will find at the top right corner of the page. \n It has a '+' on it.\n * This takes you to a new page where you will be asked to name your project.\n * On this same page you can edit your repo's \u003cb\u003eREADME.md\u003c/b\u003e which (like this file you are currently reading) records the central documentation for your project.\n * Save your changes to README.md by clicking on the \u003cb\u003eCommit Changes\u003c/b\u003e button found at the bottom right corner of the page.\n\n### Setup your computer for git \n  * \u003ccode\u003egit config --global user.name  \"your.github.account.name\"\n  * \u003ccode\u003egit config --global user.email \"you@place.com\"\u003c/code\u003e\n  * configure the \u003cb\u003ecredential.helper\u003c/b\u003e. Alas, this step differs by operating system because passwords are saved in different ways on osx, linux and windows.   Please get the right instructions for your computer at https://help.github.com/articles/set-up-git\n \n\n### Clone the project onto your own computer\n\n * cd toSomeDirectoryOfYourChoice\n * \u003ccode\u003e git clone https://github.com/Bioconductor/githubCribsheet.git\u003c/code\u003e with these results\n     * a \u003cb\u003elocal repo\u003c/b\u003e is created \n     * a \u003cb\u003eworking copy\u003c/b\u003e is created\n     * thus \u003cb\u003ethree\u003c/b\u003e versions of the code exist\n\n### Using SSH keys\n * If you want to use ssh keys instead of https to connect, see this guide: https://help.github.com/articles/generating-ssh-keys\n * The command to clone the project is then \u003ccode\u003egit clone git@github.com:Bioconductor/githubCribsheet.git\u003c/code\u003e\n\n### Overview of basic operations\n\n * Making changes to your \u003cb\u003eworking copy\u003c/b\u003e propagate them to \u003cb\u003eBOTH\u003c/b\u003e of your repos:\n    * Add some text to REAMDE.md, whose contents you originall created at the github website\n    * git diff README.md will report differences between your \u003cb\u003elocal repo\u003c/b\u003e and your \u003cb\u003eworking copy\u003c/b\u003e\n    * update the \u003cb\u003elocal repo\u003c/b\u003e:  \n        \u003ccode\u003e git commit -m \"added one line, modifying my local working copy\" README.md\u003c/code\u003e\n    * update \u003cb\u003egithub\u003c/b\u003e: \n        \u003ccode\u003e git push\u003c/code\u003e\n    * make sure your \u003cb\u003elocal repo\u003c/b\u003e and \u003cb\u003eworking copy\u003c/b\u003e have a record of the update \n      you just did to the \u003cb\u003egithub repo\u003c/b\u003e:   \u003ccode\u003egit pull\u003c/code\u003e\n\n  \n### Add a user to your project\n\n * The new user needs a github login id\n * From the project home page, click the \u003cb\u003eAdmin\u003c/b\u003e button\n * Click the \u003cb\u003eTeams\u003c/b\u003e button\n * Click the \u003cb\u003eOwners\u003c/b\u003e button\n * Enter the new user's github id\n\n### From SVN to git and back ??\n\nDoes this work? Who knows.\n\nI explored git / svn a little last night. It seems there is 'git svn'\n(separate from git but widely available), and that steps might be\n\n1. Make a repository on github, e.g., http://github.com/mtmorgan/test\n\n2. clone the svn repository locally\n\n  git svn clone \\\n      https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph\n\t  \nThis pulls in all the revision history but I think instead it might\nmake sense to limit that (e.g., to the last time the version was\nbumped during a release) by making a directory, initiating a git\nrepository, fetching a particular revision from svn, and then rebasing\nto the current version\n\t  \n    mkdir graph \u0026\u0026 cd graph\n      git svn init \\\n          https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graph\n    git svn fetch -r64680\n\tgit svn rebase\n\t\t\t\t  \nand then I see\n\t\t\t\t  \n\t$ git log --oneline\n\t4aea3d4 The following previously deprecated functions have been made\n\tb11e47e bumped version numbers after creating 2.10 branch\n\t\t\t\t  \n3. add information about the git repository\n\n    git remote add origin \\\n\t    http://github.com/Bioconductor-mentored/graph.git\n\t\t\n4. push the svn clone to github\n\n    git push -u origin master\n  \nthis gets us a github repository with a snapshot of our svn; my\nhandiwork is at\n  \n    https://github.com/mtmorgan/test\n\t\nWe could then git going on all of our revisions and finally...\n\t\n5. When done and ready to send back to Bioconductor's svn tree\n\t\n\tgit svn dcommit \n\n--\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbiocgithubhelp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbiocgithubhelp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbiocgithubhelp/lists"}