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  • TGAC Browser - Installation Guide v0.1.0/v0.1.1
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Getting Started


  • TGAC Browser requires running Apache Tomcat, Ensembl core MySQL database (i.e. Example), TGAC Browser package GitHub  and properties file (/storage/browser/tgac-browser/

Setting up


  • You will need to install MySQL v5 or greater. You will then need the latest TGAC Browser demo database dump. This is available from our repository here: tgac-browser-demo.sql
  • Log in to your local MySQL install, and create a database called 'tgac_browser_demo':

        CREATE DATABASE tgac_browser_demo'
        USE tgac_browser_demo;



  • Then populate the database with the two dumps by running the following commands at a s

    hell prompt:

     mysql -u <username> -p -D tgac_browser_demo < tgac-browser-demo.sql

 Installing and running TGAC Browser

  • You will need Maven 2.2.1 to build TGAC Browser (*NOTE Not Maven 3!*). Once you have grabbed the code and installed Maven, in the root of the project (you should see a pom.xml file and module directories like browser-web and core etc) call:

    mvn clean install command.
  • It will generate a tgac-browser.war file copy it to Apache Tomcat webapps and start the Tomcat server.
  • TGAC Browser should be running at http://<server-path>/tgac-browser

Configuring TGAC Browser

TGAC Browser overlay

  • For Customised TGAC Browser all you need is a TGAC Browser Overlay repository available here and your own property file (you can copy property file comes with demo or and edit it) placed at /storage/browser/<profile-name>/
    You need to install tgac-browser.war to local repository by

    mvn install:install-file -DartifactId=tgac-browser -Dversion=<version-number>. -Dpackaging=war -Dfile=<path-to-tgac-browser.war>/tgac-browser.war



  • you can build overlay same as main TGAC Browser with profile information i.e. mvn clean install -Dprofile=<profile-name>

  • This will take customisations from the file.

Properties file

  • TGAC Browser property file contains many features those can be changed in browser straight away
  • Standard features

    1. browser.fasta = true/false
      • turns on and off fasta features it also affects BLAST
    2. browser.title = Demo
      • you can set the Web Page Title from here
    3. browser.header = TGAC Browser Demo
      • you can set the Web Page Header from here
    4. browser.urlpath = tgac-browser
      • you can set the Web Page URL path from here
      • i.e. tgac-browser-new will be http://<server-path>/tgac-browser-new
    5. browser.defaultRef = scaffold1.1-size1749886
      • you can set the default reference from database when browser starts
  • BLAST configurations

    1. browser.blastdblink = CHO
      • sets link to TGAC Browser instance if you have more than one it should refer to browser.urlpath of other instance that you want to linked to
      • more than one BLAST dbs need corelated links seaprated by comma (,)
    2. browser.blastdblocation = /storage/browser/TGAC_CHO_v1.2_COMPLETE.fa
      • sets location for the database must be accessible to your computer and user
      • more than one BLAST dbs can be put seaprated by comma (,)
    3. browser.blastType = local/NCBI/server
      • select a blast type you want to use
      • local needs path to the BLAST+ binary file
      • server doesn't work at the moment but browser-process pipeline will support it
    4. browser.linkLocation =
    5. browser.blastLocation = /opt/blast+
      • path for BLAST+ binary files
  • Tracks from files

    1. browser.trackfiles = /storage/browser/temp.sam,/storage/browser/temp2.sam
      • specify location for .sam/.bam/.wig file
  • Database config

    1. db.driver:com.mysql.jdbc.Driver
      • jdbc driver - Don't change
    2. db.url:jdbc:mysql://
      • Mysql server location followed by database name
      • localhost can be used
    3. db.username:tgac
      • MySQL database user name
    4. db.password: pwd
      • MySQL password
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