Skip to end of metadata
Go to start of metadata

Table of content

Getting Started

Prerequisite

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

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 -Dprofile=<profile-name> -Dprofile-path=<property-file path>

  • 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

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.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
    1. browser.linkLocation = <link-to-url>
      • set-up a link to external web-database from genes, will use same name
  • Database config

    1. db.driver:com.mysql.jdbc.Driver
      • jdbc driver - Don't change
    2. db.url:jdbc:mysql://kathmandu.nbi.bbsrc.ac.uk:3306/bianx_cho_ensembl61_browser
      • Mysql server location followed by database name
      • localhost can be used
    3. db.username:tgac
      • MySQL database user name
    4. db.password: pwd
      • MySQL database password
  • No labels