Users of JBrowse should get it from the main JBrowse site at http://jbrowse.org/install.
Unless you intend to work on the JBrowse code itself, or develop a JBrowse plugin, stop reading now and go to http://jbrowse.org/install.
About running from a
Only developers should run JBrowse from a git repository. For one reason, the development version has a much, much slower initial load time than the built release zipfiles. Also, since the master branch code is ''in development'' for the next JBrowse release, it often (usually?) contains bad bugs, much more so than the official releases put up on JBrowse.org.
Setting up a development environment
Make sure you have a web server installed on your development machine. Any web server will do.
cd /my/dev/webserver/root; git clone https://github.com/GMOD/jbrowse jbrowse cd jbrowse bower --allow-root -f install ./setup.sh # and now point your browser to # http://localhost/jbrowse/index.html?data=sample_data/json/volvox # and you should see the volvox example data
Then you can simply edit files and your changes will be available in the browser (i.e. no build step is required)
You can also optionally run build steps to create the minimized codebase. Extra dependencies Text::Markdown and DateTime are required to run the build step.
make -f build/Makefile release-notest make -f build/Makefile release # alternate build with full test suite
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 npm start
Running the developer test suites
Tests for the server-side Perl code. You must have the JBrowse Perl module prerequisites installed for them to work. Run with:
prove -Isrc/perl5 -lr tests
Client-side Unit Tests
Point your browser at
You can also run them from phantomJS using
phantomjs tests/js_tests/run-jasmine.js http://my.dev.machine/jbrowse/tests/js_tests/index.html
Client-side Integration Tests
Integration tests for the client-side app. You need to have Python
nose installed. Run the tests with:
Cutting a JBrowse release
Create a directory and clone the repo: git clone --recursive https://github.com/GMOD/jbrowse.git Then for 1.12.1, git checkout tags/1.12.1-release (because it lives in a branch that is not master)
Edit the JBrowse
package.jsonfile and change 'version' to the version you are releasing. Don't commit this change to the repository, it should stay as
devin git so that it shows up in analytics as a development version.
Build the release packages:
make -f build/Makefile release. The files produced during the build should not be committed to the repository either. There is also
make -f build/Makefile release-notestfor releases that don't need perl tests to be run. NOTE: you may need to use the command
ulimit -n 1000to avoid "spawn EMFILE" build errors.
Make a tag in the repository for the release, named, e.g.
scpthe release .zip files (min and full) to jbrowse.org.
Add them to the Wordpress Downloads list so that we can track how many times they are downloaded.
Write a blog post announcing the release. The
release-notes.htmlfile made during the build might be useful for this.
Update the "Install" page on the site to point to the newest release.
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 an email announcing the release, sending to gmod-ajax, jbrowse-dev. 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.