D6.1:CCP4 integration

From West-Life
Jump to: navigation, search

M5.2: First integrated grid- or cloud- enabled X-ray service


Install the West-Life Virtual Machine

Prerequisites:

  • Install Vagrant - tool for automation of virtual machine deployment. Download and install vagrant from https://www.vagrantup.com/
  • Install Virtualbox - VM stack. Download and install virtualbox https://www.virtualbox.org/wiki/Downloads
  • download this ZIP (4kB)[1] and unzip it into some [wp6-vm directory]
  • if you are behind proxy, download and install proxyconf plugin and set environment variables
   export http_proxy=http://user:password@host:port
   export https_proxy=https://user:password@host:port
   export no_proxy=localhost
   vagrant plugin install vagrant-proxyconf
  • Open command-line (e.g. cmd, cygwin or terminal)
  cd [wp6-vm directory]
  vagrant up    

This will start a virtual machine in VirtualBox, configures port forwarding and boots CernVM 4.0 which loads Scientific Linux 7.2 and configures related West-Life work packages. Depending on the network speed, it will take several minutes to several tens of minutes - downloading 200 MB of data.

Usage:

  • The new virtual machine can be accessed by SSH (by default the 2222 port), see vagrant output whether the port wasn't changed.
   vagrant ssh
  • The virtual machine should also be listed as Running in VirtualBox. Select it, and click Show to get a desktop.
  • Then in order to add the CCP4 suite of crystallographic software, enter the following commands
  sudo bootstrap/bootstrapcvmfsccp4.sh      
  scripts/startCCP4.sh
  • The CCP4 suite is now available to run commands, and the interactive programs are available in the GUI in VirtualBox (username/password: vagrant/vagrant)
  • Files of the current working directory of host are mounted into /home/vagrant/work/local. Repositories allowing WEBDAV interface (B2DROP) are mounted into /home/vagrant/work/b2drop after input of existing b2drop account via local web interface (http://localhost:8080 by default the port 8080 is forwarded to VM).
  • For more details see [2]

Technical notes

Like some other structural biology software, the CCP4 suite is free for academic use, but is not open source. CCP4 are the sole distributors of the software, and they require the user to complete and send an academic license before running the software. Commercial users and those doing commercial work should obtain a commercial license first. See http://www.ccp4.ac.uk/ccp4license.php for further details.

The West-Life Virtual Folder is delivered as a virtual machine. It includes open source structural biology processing software. It uses the CERNVMFS in order to include large suites of software without requiring a large download or a slow startup. In this way, it relieves structural biologists of the need to download and install the software they need.

The instructions above mount a cvmfs repository with a CCP4 installation and launches the CCP4 shell at CCP4HOME/start so other ccp4 programs can be executed when typing e.g. ccp4i, coot, ccp4i2 etc.

Known Issues

  • repository facilities.gridpp.ac.uk is mounted but west-life.egi.eu may become broken, if you see Probing /cvmfs/west-life.egi.eu … Failed. “vagrant reload” from host seems to fix it.