Build research lab

Here is how to build a core research lab using our tools.

Install operating system and core tools

• 1. Set up a computer.

You can get a USB or DVD image of Centos 6.5, for example. 64 bit hardware is better, but 32 bit should work. Other linuxes have not been tested well, but Fedora should work.

• 2. Get our tools and install core packages

acquire DOCK.git from github.org

As root:

cat centos-packages | xargs yum install -y

• 3. Download, Install and Customize Python

Tested with 2.7.x We are working towards a 3.x version. This is not absolutely necessary, but we find it is more reliable to have complete control. as root:

./python.sh path-to-python-tarball /opt/python

• 4. Acquire and Install RDKit

Get RDKit from:

http://sourceforge.net/projects/rdkit/files/rdkit/

Install RDKit using:

blah blah blah

• 5. Use pip to get critical tools

Use the following to get numpy, scipy, biopython, psycopg2, MySQL-python, sh, matplotlib

/opt/python/bin/pip install -r requirements.txt 
pip install flask
pip install sqlalchemy
pip install flask-admin

• 6. Get UCSF Software

get rdalchemy.git
get AgAd demo  and data from git

• 7. Global update of all software.

yum update

testing

• 1 . Start the default cheminformatics web server.

• 2. run DOCK tests

• 3. Download custom subset of ZINC

Please note that optional infrastructure such as Queuing system, NFS server layout, puppet, libvirt and foreman are described separately, since you are able to run a full lab without any of them, just not very efficiently.