To install JBrowse, see the main JBrowse wiki at http://gmod.org/wiki/JBrowse.
The rest of this file is aimed primarily at developers.
About running from a
Unless you are actively working or collaborating on the JBrowse code, you should not run JBrowse from a git repository. For one reason, it 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 has a lot more bugs than the official releases. Be warned.
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 --recursive email@example.com:YOURACCOUNT/jbrowse.git cd jbrowse ./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
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 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:
The embedded documentation is written in JSDoc. See http://code.google.com/p/jsdoc-toolkit.
bin/jbdoc ArrayRepr will open your browser with
documentation about ArrayRepr.js.
The here for a comprehensive list of JSDoc tags.
Cutting a JBrowse release
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.
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.