To install jbrowse, visit http://jbrowse.org/blog and download the latest JBrowse zip file. See instructions at http://jbrowse.org/docs/installation.html for a tutorial on setting up a sample instance.
Install JBrowse from GitHub (for developers)
To install from GitHub, you can simply clone the repo and run the setup.sh script
git clone https://github.com/GMOD/jbrowse cd jbrowse ./setup.sh
Develop JBrowse or JBrowse plugins
To start modifying jbrowse code, you can run something like this
git clone https://github.com/GMOD/jbrowse cd jbrowse ./setup.sh # not strictly necessary if you don't need to sample data yarn yarn watch
yarn watch running in the background as you create changes to your code. You can also run
yarn start in another window and that will launch a webserver running jbrowse, or you can just have the jbrowse folder in your webserver directory. The key is to run yarn watch while you are editing code so that webpack incorporates your changes in either the main codebase (src/JBrowse folder) or any plugins (plugins/YourPlugin).
Note for users in China
In order to make downloads faster you can set a mirror for the npm registry
npm config set registry http://r.cnpmjs.org npm config set puppeteer_download_host=http://cnpmjs.org/mirrors export ELECTRON_MIRROR="http://cnpmjs.org/mirrors/electron/"
Notes on setting up a JBrowse server
If you don't have a webserver such as apache or nginx, you can run
npm run startand open http://localhost:8082/index.html?data=sample_data/json/volvox to see the code running from a small express.js server.
You can alternatively just move the jbrowse folder into a nginx or apache root directory e.g. /var/www/html and then navigate to http://localhost/jbrowse
Note: you should avoid using sudo tasks like ./setup.sh and instead use chown/chmod on folders to your own user as necessary.
Also note: After editing a file, you must re-run the webpack build with
npm run build or you can keep webpack running in "watch" mode by running
npm run watch.
Also also note: by default
git clone will clone the master branch which contains the latest stable release. The latest development branch is called dev. Run
git checkout dev after clone to retrieve this
Installing as an npm module
To install jbrowse from NPM directly, you can run.
npm install @gmod/jbrowse
To setup a simple instance, you can use
Looking for places to contribute to the codebase? Check out the "help wanted" label.
Running the developer test suites
prove -Isrc/perl5 -lr tests node tests/js_tests/run-puppeteer.js http://localhost/jbrowse/tests/js_tests/index.html pip install selenium nose MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests
Supported browsers for SELENIUM_BROWSER are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'. The Sauce Labs + Travis one will only work in a properly configured Travis CI build environment.
JBrowse has a free open source account on Browserstack for manual testing. Contact @rbuels for access.
Generating Packaged Builds
You can also optionally run build steps to create the minimized codebase. Extra perl dependencies Text::Markdown and DateTime are required to run the build step.
make -f build/Makefile
To build the Electron app (JBrowse desktop app), run the following
npm install -g electron-packager make -f build/Makefile release-electron-all
To run the Electron app in debug mode run the following
npm install -g electron electron browser/main.js
Making a JBrowse release
NOTE: Beginning in 1.12.4,
build/release.sh $newReleaseVersion $nextReleaseVersion-alpha.0 notes.txt, where notes.txt is any additional information to add to a blogpost. Then check its work, and then run the
git pushcommand it suggests to you. This makes a tag in the repository for the release, named, e.g.
1.6.3-release. This should cause Travis CI to create a release on GitHub under https://github.com/GMOD/jbrowse/releases
Test that the page loads in IE11 on BrowserStack
Add release notes to the new GitHub release that Travis created. Can just paste these from release-notes.md, which is in Markdown format.
Write a twitter post for usejbrowse and JBrowseGossip with the announcement link to the blogpost
Write an email announcing the release, sending to gmod-ajax. If it is a major release, add gmod-announce and make a GMOD news item.
As you can tell, this process could really use some more streamlining and automation.