https://github.com/gmod/jbrowse
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
https://github.com/gmod/jbrowse
bioinformatics biology genome-annotation genome-browser genomics protein-annotation
Last synced: 8 days ago
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JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
- Host: GitHub
- URL: https://github.com/gmod/jbrowse
- Owner: GMOD
- License: other
- Created: 2009-01-16T11:30:52.000Z (over 16 years ago)
- Default Branch: master
- Last Pushed: 2025-03-19T14:22:24.000Z (about 1 month ago)
- Last Synced: 2025-04-06T05:04:05.228Z (15 days ago)
- Topics: bioinformatics, biology, genome-annotation, genome-browser, genomics, protein-annotation
- Language: JavaScript
- Homepage: http://jbrowse.org
- Size: 67.2 MB
- Stars: 468
- Watchers: 51
- Forks: 198
- Open Issues: 170
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
[](CODE_OF_CONDUCT.md)
Note: most of our current development is on JBrowse 2, see our github repo here
https://github.com/gmod/jbrowse-components
We will still continue to make bug fix and maintenance releases of JBrowse 1 but
most development is on JBrowse 2
Note: if you are using plugins with a dev version of JBrowse or installing from
GitHub, you may need to use node <=14 (e.g. node >=15 may fail) due to node-sass
not compiling on newer node versions easily. See
https://github.com/GMOD/jbrowse/pull/1607 for details
# Installing JBrowse
To install jbrowse, visit http://jbrowse.org/blog and download the latest
JBrowse zip file. See instructions at http://jbrowse.org/docs/installation.html
for a tutorial on setting up a sample instance.
# 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
## Develop JBrowse or JBrowse plugins
To obtain a jbrowse development environment, e.g. for jbrowse source code
editing or plugin development (or just running jbrowse from the github repo)
git clone https://github.com/GMOD/jbrowse
cd jbrowse
./setup.sh # not strictly necessary if you don't need to sample data
If you are going to edit the jbrowse source code, then also run
yarn watch
And keep `yarn watch` running in the background as you create changes to your
code.
To start a temporary dev server, can also run
yarn start
And keep this running in the background, this will launch a webserver running
jbrowse on port 8082.
Alternatively, you can put this jbrowse folder in your webserver (e.g.
/var/www/html/) directory. The key is, if you are modifying jbrowse or plugin
source code, to run `yarn watch` in the background, so that webpack incorporates
your changes in either the main codebase (src/JBrowse folder) or any plugins
(plugins/YourPlugin).
## Note for users in China
In order to make downloads faster you can set a mirror for the npm registry
npm config set registry http://r.cnpmjs.org
npm config set puppeteer_download_host=http://cnpmjs.org/mirrors
export ELECTRON_MIRROR="http://cnpmjs.org/mirrors/electron/"
## Notes on setting up a JBrowse server
- If you don't have a webserver such as apache or nginx, you can run
`npm run start` and open
http://localhost:8082/index.html?data=sample_data/json/volvox to see the code
running from a small express.js server.
- You can alternatively just move the jbrowse folder into a nginx or apache root
directory e.g. /var/www/html and then navigate to http://localhost/jbrowse
_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
node tests/js_tests/run-puppeteer.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
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 notes.txt`,
where notes.txt is any additional information to add to a blogpost. Then
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. Test that the page loads in IE11 on BrowserStack
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. Write a twitter post for usejbrowse and JBrowseGossip with the announcement
link to the blogpost
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.