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

    hell prompt:

    Info
     mysql -u <username> -p -D tgac_browser_demo < tgac-_browser-_demo.sql
  • Log in to your local MySQL install, and create a database called 'tgac_browser_blast_manager':

    Info
        CREATE DATABASE tgac_browser_blast_manager'
        USE tgac_browser_blast_manager;

     

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

    hell prompt:

    Info
     mysql -u <username> -p -D tgac_browser_blast_manager < tgac_browser_blast_manager.sql
  •  

 Installing and running TGAC Browser

...

  • 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
  • BAST Database config

    1. blast_db.driver:com.mysql.jdbc.Driver
      • jdbc driver - Don't change
    2. blast_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. blast_db.username:tgacbrowser
      • MySQL database user name
    4. blast_db.password: pwd
      • MySQL database password

  • Tracks from files

    1. browser.trackfiles = /storage/browser/temp.sam,/storage/browser/temp2.sam
      • specify location for .sam/.bam/.wig file
  • Tracks from files

    1. Now tracks can be added from ensembl database

      source = file and file path = location of file

      web_data in analysis_description

       

      {
      "colour""blue",
      "source""file",
      "filepath""/storage/browser/data/LIB1777_nonrrna_accepted_hits_sort_Reverse_norm_neg.bw",
      "group-name": LIB1777,
      }