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Update VMBiskit

Before serious use, we recommend that you bring both Biskit and the Ubuntu OS up to date.

Updating the VMBiskit machine

  1. Update the Operating system:

    sudo aptitude update
    sudo aptitude upgrade
  2. Update the biskit installation:

    cd ~/py/biskit
    svn update
  3. Install databases:

    VMBiskit comes without the PFam and Blast databases to keep its size manageable. Before using Conservation profile method (PDBDope.addConservation) you need to download and install the Pfam database:

    Before using the homology modeling pipeline you need to download and install the blast database (and also the Modeller program):

    • follow the instructions in setup Blast (skip point 1, the NCBI toolkit is already installed)

    A better option would be if you would mount an existing folder with these databases into the virtual machine. For that you have to edit /etc/fstab. [Put in detailed instructions]

  4. Change password:


    Since everyone can look up the original password on this web site, this may be a good idea...

Good luck!