Build research lab: Difference between revisions
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(Created page with "Here is how to build a core research lab using our tools. = install operating system and core tools = * 1. Set up a computer. e.g. Centos 6.5 * 2. Get out tools DOCK.git ...") |
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Here is how to build a core research lab using our tools. | Here is how to build a core research lab using our tools. | ||
= | = Install operating system and core tools = | ||
* 1. Set up a computer. | * 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 | * 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 Python 2.7 | * 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 | ./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 = | = testing = | ||
* 1 . Start the default cheminformatics web server. | |||
* 2. run DOCK tests | |||
* 2. run DOCK | |||
* 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. | |||
[[Category:Sysadmin]] | [[Category:Sysadmin]] | ||
Latest revision as of 04:22, 1 October 2015
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.