To install jbrowse, most users should visit http://jbrowse.org/install and download a zip file such as JBrowse-1.13.0.zip. See instructions at https://jbrowse.org/code/latest-release/docs/tutorial/ for a tutorial on setting up a sample instance.
Once you have an instance up and running, http://gmod.org/wiki/JBrowse_Configuration_Guide is the comprehensive reference guide to JBrowse configuration.
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
At this point, if you are in the web root of your Apache or nginx folder, you can access it as http://localhost/jbrowse/?data=sample_data/json/volvox
utils/jb_run.js -p 3000 and access http://localhost:3000/index.html?data=sample_data/json/volvox
to see the code running from a small express.js server.
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 phantomjs tests/js_tests/run-jasmine.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
Add release notes to the new GitHub release that Travis created. Can just paste these from release-notes.md, which is in Markdown format.
Update the latest-release code checkout on the site, which the "Latest Release" demo on the jbrowse.org points to, to be an unzipped-and-set-up copy of the latest release.
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.