{"id":13510140,"url":"https://github.com/GMOD/jbrowse","last_synced_at":"2025-03-30T15:30:47.393Z","repository":{"id":482938,"uuid":"108695","full_name":"GMOD/jbrowse","owner":"GMOD","description":"JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. 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See\nhttps://github.com/GMOD/jbrowse/pull/1607 for details\n\n# Installing JBrowse\n\nTo install jbrowse, visit http://jbrowse.org/blog and download the latest\nJBrowse zip file. See instructions at http://jbrowse.org/docs/installation.html\nfor a tutorial on setting up a sample instance.\n\n# Install JBrowse from GitHub (for developers)\n\nTo install from GitHub, you can simply clone the repo and run the setup.sh\nscript\n\n    git clone https://github.com/GMOD/jbrowse\n    cd jbrowse\n    ./setup.sh\n\n## Develop JBrowse or JBrowse plugins\n\nTo obtain a jbrowse development environment, e.g. for jbrowse source code\nediting or plugin development (or just running jbrowse from the github repo)\n\n    git clone https://github.com/GMOD/jbrowse\n    cd jbrowse\n    ./setup.sh # not strictly necessary if you don't need to sample data\n\nIf you are going to edit the jbrowse source code, then also run\n\n    yarn watch\n\nAnd keep `yarn watch` running in the background as you create changes to your\ncode.\n\nTo start a temporary dev server, can also run\n\n    yarn start\n\nAnd keep this running in the background, this will launch a webserver running\njbrowse on port 8082.\n\nAlternatively, you can put this jbrowse folder in your webserver (e.g.\n/var/www/html/) directory. The key is, if you are modifying jbrowse or plugin\nsource code, to run `yarn watch` in the background, so that webpack incorporates\nyour changes in either the main codebase (src/JBrowse folder) or any plugins\n(plugins/YourPlugin).\n\n## Note for users in China\n\nIn order to make downloads faster you can set a mirror for the npm registry\n\n    npm config set registry http://r.cnpmjs.org\n    npm config set puppeteer_download_host=http://cnpmjs.org/mirrors\n    export ELECTRON_MIRROR=\"http://cnpmjs.org/mirrors/electron/\"\n\n## Notes on setting up a JBrowse server\n\n- If you don't have a webserver such as apache or nginx, you can run\n  `npm run start` and open\n  http://localhost:8082/index.html?data=sample_data/json/volvox to see the code\n  running from a small express.js server.\n\n- You can alternatively just move the jbrowse folder into a nginx or apache root\n  directory e.g. /var/www/html and then navigate to http://localhost/jbrowse\n\n_Note: you should avoid using sudo tasks like ./setup.sh and instead use\nchown/chmod on folders to your own user as necessary._\n\n_Also note: After editing a file, you must re-run the webpack build with\n`npm run build` or you can keep webpack running in \"watch\" mode by running\n`npm run watch`._\n\n_Also also note: by default `git clone` will clone the master branch which\ncontains the latest stable release. The latest development branch is called dev.\nRun `git checkout dev` after clone to retrieve this_\n\n# Installing as an npm module\n\nTo install jbrowse from NPM directly, you can run.\n\n    npm install @gmod/jbrowse\n\nTo setup a simple instance, you can use\n\n    node_modules/.bin/jb_setup.js\n    node_modules/.bin/jb_run.js\n\nThen visit http://localhost:3000/?data=sample_data/json/volvox\n\n# Contributing\n\nLooking for places to contribute to the codebase?\n[Check out the \"help wanted\" label](https://github.com/GMOD/jbrowse/labels/help%20wanted).\n\n# Running the developer test suites\n\nThe Travis-CI suite runs Perl, JavaScript, and Selenium automated tests. To run\nlocally, you can use\n\n    prove -Isrc/perl5 -lr tests\n    node tests/js_tests/run-puppeteer.js http://localhost/jbrowse/tests/js_tests/index.html\n    pip install selenium nose\n    MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests\n\nSupported browsers for SELENIUM_BROWSER are 'firefox', 'chrome', 'phantom', and\n'travis_saucelabs'. The Sauce Labs + Travis one will only work in a properly\nconfigured Travis CI build environment.\n\n# Manual testing\n\n\u003cimg style=\"display: block; margin: 1em auto\" src=\"img/browserstack-logo-600x315.png\" width=\"200\" alt=\"Browserstack\"/\u003e\n\nJBrowse has a free open source account on\n[Browserstack](http://browserstack.com/) for manual testing. Contact @rbuels for\naccess.\n\n# Generating Packaged Builds\n\nYou can also optionally run build steps to create the minimized codebase. Extra\nperl dependencies Text::Markdown and DateTime are required to run the build\nstep.\n\n    make -f build/Makefile\n\nTo build the Electron app (JBrowse desktop app), run the following\n\n    npm install -g electron-packager\n    make -f build/Makefile release-electron-all\n\nTo run the Electron app in debug mode run the following\n\n    npm install -g electron\n    electron browser/main.js\n\n# Making a JBrowse release\n\nNOTE: Beginning in 1.12.4,\n\n1. Run\n   `build/release.sh $newReleaseVersion $nextReleaseVersion-alpha.0 notes.txt`,\n   where notes.txt is any additional information to add to a blogpost. Then\n   check its work, and then run the `git push` command it suggests to you. This\n   makes a tag in the repository for the release, named, e.g. `1.6.3-release`.\n   This should cause Travis CI to create a release on GitHub under\n   https://github.com/GMOD/jbrowse/releases\n\n1. Test that the page loads in IE11 on BrowserStack\n\n1. Add release notes to the new GitHub release that Travis created. Can just\n   paste these from release-notes.md, which is in Markdown format.\n\n1. Write a twitter post for usejbrowse and JBrowseGossip with the announcement\n   link to the blogpost\n\n1. Write an email announcing the release, sending to gmod-ajax. If it is a major\n   release, add gmod-announce and make a GMOD news item.\n\nAs you can tell, this process could really use some more streamlining and\nautomation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FGMOD%2Fjbrowse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FGMOD%2Fjbrowse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FGMOD%2Fjbrowse/lists"}