GBiB: From download to BLAT at assembly hubs

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".
  • General ---> Advanced ---> Drag'n'Drop: Bidirectional.
  • General ---> Description: Schistosoma mansoni genome assembly and track hubs.
  • System ---> Motherboard ---> Base Memory: 4.096 MB.
  • System ---> Processor ---> Processor(s): 2.
  • Display ---> Video ---> Video Memory: 32 MB.
  • Shared Folders ---> + ---> Folder Path: /usr/local/src/gbib/hub/ ---> Auto-mount ---> OK.
• Boot GBiB virtual machine:
  • Select "browserbox" on menu at left.
  • Click at "Start".
• Test if everything is working at the following URLs:
  • http://127.0.0.1:1234
  • http://127.0.0.1:1234/folders
• Login using ssh, for a faster access.
  • Open a terminal, like "konsole".
  • Password: browser

    $> ssh browser@localhost -p 1235

• Install tools that allows file manipulations:

    $> gbibAddTools

• Turn off every kind of automatic update:

    $> gbibAutoUpdateOff

• Do not allow users to mirror tracks:

    $> gbibMirrorTracksOff

• Turn on the offline mode:

    $> gbibOffline

• Reboot the virtual machine

    $> sudo shutdown -r now

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