CELPP Virtual Machine

This page describes steps to spin up a virtual machine capable of running CELPP with non-commercial software already installed.

Requirements

• Linux or Mac os
• Vagrant
• Virtualbox
• Git command line tools
• At least 4gb ram

Step 1 Download D3R repo

Open a terminal and issue the following commands:

git clone https://github.com/drugdata/D3R.git
cd D3R/vagrant/centos7

Step 2 Spin up virtual machine using Vagrant

This step can take a while (10+ minutes)

vagrant up

Step 3 connect via ssh to virtual machine

vagrant ssh

What did I just do?

With the above command vagrant ssh the terminal should be connected to the virtual machine that was just created. This virtual machine has the following software installed on Centos 7 using the configuration in the Puppet-D3R repo:

• pymol put in /opt/pymol
• rdkit 2016.03.3 setup in miniconda located in /opt/miniconda2
• Unlicensed Openeye Python toolkit under default python install
• NCBI blast put in /usr/bin
• AutoDock Vina in /opt/autodock_vina_1_1_2_linux_x86/bin
• MGLTools in /usr/local/mgltools (Be sure to set MGL_ROOT=/usr/local/mgltools)

Step 4 shutting down virtual machine

# exit from virtual machine, assuming you ran step 3 command
exit
vagrant destroy

NOTE: vagrant halt will stop the machine, but not destroy it.