JBlast - A BLAST service for JBConnect and JBrowse
JBlast (jblast-jbconnect-hook) is JBConnect hook module. It contains both server-side integration with JBConnect and JBrowse that enables Blast analysis that is tightly integrated with JBrowse. JBlast can execute stand-alone NCBI blast commands directly, or it can be configured to use Galaxy for workflow processing. Through the JBrowse user interface the user can choose to submit an existing feature as a blast query or highlight a region to blast. The user can monitor blast execution processing through JBConnect’s job queue and the blast search results will appear directly as an inserted track in the track selector.
JBlast User Quick Tutorial
JBlast provides the following functionality:
|Can leverage Galaxy Server for Blast Analysis or use stand-alone NCBI Blast tools|
|Basic workflow abstraction and Monitoring|
The Client-Side JBlast plugin intgration with JBrowse:
|Submit region or existing feature for blast search|
|Inject result tracks into existing configuration with persistence.|
|Dynamically filter Blast results and save results.|
|Extended feature details with blast results|
Instructions for installing JBlast with stand-alone NCBI Blast tools (non-Galaxy).
To setup Galaxy integration, see `Configure JBConnect with Galaxy`_
(Since JBConnect is generally intended to be a companion of JBrowse. JBrowse may also be installed in a separate directory. (See jbs-separate-dir.)
To integrate with Galaxy, see Setup Galaxy.
Install redis and sails
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.
# 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 @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 (default login: juser/password).
- Configuration Options
- Setup Galaxy