@gmod/jbrowse/README.md

JBrowse - client-side genome browser

[![Build status](https://travis-ci.org/GMOD/jbrowse.svg?branch=dev)](https://travis-ci.org/GMOD/jbrowse)

# Installing JBrowse

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

Alternatively, run `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

    node_modules/.bin/jb_setup.js
    node_modules/.bin/jb_run.js

Then visit http://localhost:3000/?data=sample_data/json/volvox


# Contributing

Looking for places to contribute to the codebase?
[Check out the "help wanted" label](https://github.com/GMOD/jbrowse/labels/help%20wanted).

# Running the developer test suites

The Travis-CI suite runs Perl, JavaScript, and Selenium automated tests. To run locally, you can use

    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.

# Manual testing

<img style="display: block; margin: 1em auto" src="img/browserstack-logo-600x315.png" width="200" alt="Browserstack"/>

JBrowse has a free open source account on [Browserstack](http://browserstack.com/) 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,

1. Run `build/release.sh $newReleaseVersion $nextReleaseVersion-alpha.0`, check its work, and then run the `git push` command 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

1. Add release notes to the new GitHub release that Travis created. Can just paste these from release-notes.md, which is in Markdown format.

1. Edit a file in website/blog/ folder with the date and release name in the blog title. Include notes from release-notes.md and links to files that were generated in the release page. The SHA1 sums of the built release files can be seen near the end of the Travis build log. Commit this blog post with "[update docs]" in the commit message

1. 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.

1. Write a twitter post for usejbrowse and JBrowseGossip with the announcement link to the blogpost

1. Upload the release package to the website code directory, unzip and set the version as the latest

1. 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.