JBlast BLAST/Galaxy - JBrowse Server Hook

Full documentation w/ Galaxy integration: Installation & Demo Setup

Pre-Install

JBlast requires redis as a pre-requisite, which is only used by the queue framework (kue). JBConnect depends on Sails.js.

Install redis and sails

yum install redis
redis-server
npm install -g sails@1.0.2

Install

Install the JBConnect and JBrowse. jb_setup.js ensures the sample data is loaded.

# install jbconnect
git clone http://github.com/gmod/jbconnect
cd jbconnect
npm install

# install blast tools and sample data
npm install enuggetry/blast-ncbi-tools enuggetry/faux-blastdb

# pull in NCBI blast executables
./utils/blast_getBlastUtils.js 2.8.1

# install jblast
npm install gmod/jblast-jbconnect-hook

# install jbrowse & setup jbrowse demo
npm install @gmod/jbrowse@1.15.1
patch node_modules/@gmod/jbrowse/setup.sh fix_jbrowse_setup.patch
./utils/jb_setup.js

# register plugins
./jbutil --pushplugins --buildwebpack

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.

Run

Launch the server.

sails lift

From a web browser, access the application (default login: juser/password).

http://localhost:1337/jbrowse?data=sample_data/json/volvox
or http://localhost:1337/login