Build research lab: Difference between revisions
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This is not absolutely necessary, but we find it is more reliable to have complete control. as root: | 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 | ./python.sh path-to-python-tarball /opt/python | ||
* 4. | * 4. Acquire and Install Rdkit | ||
Get rdkit from: | |||
http://sourceforge.net/projects/rdkit/files/rdkit/ | |||
Install Rdkit using: | |||
blah blah blah | |||
* 5. | * 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 flask | ||
pip install sqlalchemy | pip install sqlalchemy | ||
pip install flask-admin | pip install flask-admin | ||
* | * 6. Get UCSF Software | ||
get rdalchemy.git | get rdalchemy.git | ||
get AgAd demo and data from git | get AgAd demo and data from git | ||
* | * 7. Global update of all software. | ||
yum update | yum update | ||
Revision as of 19:43, 21 October 2014
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.