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Modern JavaScript-based Genome Browser

README.md

Installing JBrowse

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 git repository

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 git@github.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

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

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:

JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests

Using the embedded JavaScript documentation

The embedded documentation is written in JSDoc. See http://code.google.com/p/jsdoc-toolkit.

Running 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

  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.

  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.

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