Paper: JBrowse Connect: A server API to connect JBrowse instances and users, Yao, Buels, Stein, Sen, Holmes, et al. 2020; PLOS Computational Biology
JBConnect provides the following features:
|Sails JS - NodeJS/Expressed-based|
|Tightly integrated with JBrowse|
Track & Dataset Management with JBrowse integration
|Flexible Authentication – (Passport.js) supporting strategies, like OAuth2, OpenID, etc.|
|User management services|
|Policy Engine f0r managing access to Tracks, Datasets, Services, Assets|
|Extensible server-side analysis with workflow abstraction and job queue|
|Waterline ORM (MongoDB, MySQL, Postgres, Redis, etc.) with integrated Blueprint object models|
|npm installable hook model supporting both client-side (JBrowse plugins) and server-side extensions in a single package.|
|Grunt – task management (minification, watches, etc.)|
The quick start instructions demonstrate installing JBConnect with JBrowse loaded as a an NPM module (since JBConnect is generally intended to be a companion of JBrowse. JBrowse may also be installed in a separate directory. (See JBrowse Installed In Separate Directory.)
yum install redis redis-server npm install -g firstname.lastname@example.org
Install the JBConnect and JBrowse. jb_setup.js ensures the sample data is loaded.
git clone http://github.com/gmod/jbconnect cd jbconnect npm install npm install @email@example.com patch node_modules/@gmod/jbrowse/setup.sh fix_jbrowse_setup.patch ./utils/jb_setup.js
The patch operation is needed to make JBrowse 1.15.1 setup.sh run properly. If JBrowse is installed in another location, the patch should be run before setup.sh.
Launch the server.
From a web browser, access the application.
You will arrive at the following screen
The default username/password: juser/password
npm currently reports a number of vulnerability warnings of various degrees of severity, most of which are coming from Sails. Many of these warnings are fixed in a later version of SailsJS. We hope in a future release of the software to correct more of these warnings.
- Configuration Options
- JBConnect Hooks