Biskit Virtual Machine
Download and install the free VMWare Server or Player for your platform from:
Download the vmbiskit snapshot -- pending --
Unpack the snapshot
tar jvfx vmbiskit_ubuntuserver.tar.bz2
On Windows: Find an archiving tool -- tell me which one supports bzip2!
Open the virtual machine in VMWare
- File / Open / Browse -> vmbiskit_ubuntuserver/
- login with user name biskit and password biskit
Connect to the virtual machine
The vmbiskit snapshot is a text-only installation but it can 'forward' graphical x11 windows to your host computer. The system is configured to fetch a dynamic IP address from DHCP (modify these settings in /etc/network/interfaces). To access it from outside, you need to know which IP address was assigned to it.
on vmbiskit: read the IP address with ifconfig:
vmbiskit|~> ifconfig eth0 Link encap:Ethernet HWaddr 00:0C:29:4F:52:46 inet addr:192.168.116.131 Bcast:192.168.116.255 Mask:255.255.255.0 inet6 addr: fe80::20c:29ff:fe4f:5246/64 Scope:Link ...
Note the address given after 'inet addr:'
Now connect to the vmbiskit machine from your host:
Replace '192.168.116.131' with the address noted above.
And check that you can open graphical windows:
If pymol doesn't open, try to re-connect with 'ssh -X firstname.lastname@example.org'
Working with the VMBiskit machine
The Biskit project is installed locally in ~/biskit. The Biskit scripts are in the search PATH.
Updating the VMBiskit machine
Update the Operating system:
sudo aptitude upgrade
Update the biskit installation:
cd ~/py/biskit svn update
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:
- follow the instructions in setup Pfam
Before using the homology modeling pipeline you need to download and install the blast database:
- 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]