rokhayaba / jbrowse

A modern genome browser built with JavaScript and HTML5.

Installing JBrowse

Users of JBrowse should get it from the main JBrowse site at http://jbrowse.org/install where official release are available.

It is generally recommended that installing from the master branch is for development purposes. One reason is because the development version has a much slower initial load than the Release package. Also, since the master branch code is ''in development'' for the next JBrowse release, it may contain bugs.

Install from github repo (development)

Note: jb_run.js is a built-in express server that serves JBrowse. However, any webserver like Apache or NGINX can be used.

If you are using a 3rd party webserver, you should clone JBrowse into your web root

git clone https://github.com/GMOD/jbrowse
cd jbrowse
npm install
./jb_setup.js   (optional -- sets up demo files such as Volvox)
./jb_run.js     (optional -- begin serving JBrowse with built-in mini web server)

If you have installed the demo (with ./jb_setup.js), you can point your browser to http://localhost/jbrowse/index.html?data=sample_data/json/volvox and you should see the volvox example data.

Now you can simply edit files and your changes will be available in the browser (the build step is not required).

Installing as an npm module

This allows JBrowse to be easily integrated into other applications. jb_setup.js and jb_run.js are copied into the application root and can be used to install the demo files and serve JBrowse, respectively.

npm install GMOD/jbrowse

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 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 -g electron
electron browser/main.js

Running the developer test suites

Server-side Perl

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 http://my.dev.machine/jbrowse/tests/js_tests/index.html

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 eggs for selenium and nose installed. Run the tests with:

MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests

Supported browsers are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'. The Sauce Labs + Travis one will only work properly in a properly configured Travis CI build environment.

Cutting a JBrowse release

1. Edit the JBrowse package.json file and change 'version' to the version you are releasing. Don't commit this change to the repository, it should stay as dev in git so that it shows up in analytics as a development version.

2. 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-notest for releases that don't need perl tests to be run. NOTE: you may need to use the command ulimit -n 1000 to avoid "spawn EMFILE" build errors.

3. Make a tag in the repository for the release, named, e.g. 1.6.3-release.

4. scp the release .zip files (min and full) to jbrowse.org.

5. Add them to the Wordpress Downloads list so that we can track how many times they are downloaded.

6. Write a blog post announcing the release. The release-notes.html file made during the build might be useful for this.

7. Update the "Install" page on the site to point to the newest release.

8. 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.

9. 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.