GBiB: From download to BLAT at assembly hubs

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GBiB installation

  • Create a folder at your machine to place the installation files:
    $> sudo mkdir /usr/local/src/gbib


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