GBiB: From download to BLAT at assembly hubs

From genomewiki
Jump to navigationJump to search

GBiB installation

  • Create a folder at your machine to place the installation files:
    $> sudo mkdir /usr/local/src/gbib
  • Log in at UCSC Genome Browser virtual store:
    • Genome Store
    • Click in "Add to cart" at the box relative to GBiB.
    • Click in "My products" on menu.
    • Note the download address.
    • Download GBiB to /usr/local/src/gbib:
    $> sudo wget https://genome-store.ucsc.edu/media/products/gbib.zip
  • Uncompress and delete gbib.zip:
    $> unzip gbib.zip
    $> rm gbib.zip
  • Start VirtualBox:
    $> sudo virtualbox &
  • Add GBiB to VirtualBox:
    • Machine ---> Add ---> /usr/local/src/gbib/browserbox.vbox ---> Start
    • Wait while the first update is done.
    • Close GBiB terminal window.
    • Select "Send the shutdown signal".
    • Confirm by clicking "OK".


GBiB Configuration

  • Click at "Settings".


Assembly hub configuration

  • Log in again using ssh:
    $> ssh browser@localhost -p 1235


Track hub configuration

  • Create the contents of trackDb.txt:
    $> sudo cat > /usr/local/share/gbib/hubs/geneNetwork/schMan2/trackDb.txt << EOI
    track SMPs
    
    EOI


Blat configuration

  • From the folder that contains the .2bit file, start two gfServer's, specifying the assembly hub ports that will be used to access the DNA sequence and the aminoacids sequence:
    $> gfServer start 127.0.0.1 42422 -stepSize=5 schMan2.2bit &
    $> gfServer start 127.0.0.1 42423 -trans schMan2.2bit &


Custom track configuration

    track type=bigBed


GBiB maintenance

  • Make an update of all softwares and data:
    $> gbibOnline