Build research lab - Revision history

Frodo: asdf

2015-10-01T04:22:09Z

asdf

← Older revision		Revision as of 04:22, 1 October 2015
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	./python.sh path-to-python-tarball /opt/python		./python.sh path-to-python-tarball /opt/python

	* 4. Acquire and Install ~~Rdkit~~		* 4. Acquire and Install [[RDKit]]
	Get ~~rdkit~~ from:		Get RDKit from:
	http://sourceforge.net/projects/rdkit/files/rdkit/		http://sourceforge.net/projects/rdkit/files/rdkit/
	Install ~~Rdkit~~ using:		Install RDKit using:
	blah blah blah		blah blah blah

Frodo: /* Install operating system and core tools */

2014-10-21T19:43:04Z

Install operating system and core tools

← Older revision		Revision as of 19:43, 21 October 2014
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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
	~~run install ez_setup.py setuptools to new python install~~

	* 4. ~~Use ezinstall to add pip~~		* 4. Acquire and Install Rdkit
	~~command here~~		Get rdkit from:
			http://sourceforge.net/projects/rdkit/files/rdkit/
			Install Rdkit using:
			blah blah blah

	* 5. ~~Install latest Postgres~~		* 5. Use pip to get critical tools
	~~yum install psql~~		Use the following to get numpy, scipy, biopython, psycopg2, MySQL-python, sh, matplotlib
			/opt/python/bin/pip install -r requirements.txt
	* 6. Get latest Rdkit
	get ~~rdkit.~~

	* 7 Use ~~pip~~ to get ~~tools~~
	pip install flask		pip install flask
	pip install sqlalchemy		pip install sqlalchemy
	pip install flask-admin		pip install flask-admin

	* ~~8. Get our tools~~		* 6. Get UCSF Software

	* 9. Get UCSF Software
	get rdalchemy.git		get rdalchemy.git

	get AgAd demo and data from git		get AgAd demo and data from git

	* 10. Global update of all software		* 7. Global update of all software.
	yum update		yum update

Frodo at 18:54, 21 October 2014

2014-10-21T18:54:16Z

← Older revision		Revision as of 18:54, 21 October 2014
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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 =		= 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.		You can get a USB or DVD image of Centos 6.5, for example. 64 bit hardware is better, but 32 bit should work.
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	= testing =		= testing =

			* 1 . Start the default cheminformatics web server.

	* 1 . ~~set up a 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.
	= optional ~~set up =~~
	* 1. queuing system

	* 2. nfs server and ~~central services~~

	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Frodo: /* install operating system and core tools */

2014-10-21T18:51:36Z

install operating system and core tools

← Older revision		Revision as of 18:51, 21 October 2014
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	= install operating system and core tools =		= install operating system and core tools =
	* 1. Set up a computer. ~~e.g.~~ Centos 6.5		* 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 ~~out~~ tools DOCK.git		* 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 ~~tarball~~		* 3. Download, Install and Customize Python
			Tested with 2.7.x We are working towards a 3.x version.
	* 4. ~~cat centos-packages \| xargs yum install -y~~		This is not absolutely necessary, but we find it is more reliable to have complete control. as root:

	* 5. ~~yum update - global update of all software~~

	* 6. ~~install python~~
	./python.sh path-to-python-tarball /opt/python		./python.sh path-to-python-tarball /opt/python
			run install ez_setup.py setuptools to new python install

	* 7. ~~run install ez_setup.py setuptools to new python install~~		* 4. Use ezinstall to add pip
			command here
	* 8. use ezinstall to add pip

	* 9. yum install psql		* 5. Install latest Postgres
			yum install psql

	* 10. get rdkit.		* 6. Get latest Rdkit
			get rdkit.

	* ~~11.~~ pip install flask		* 7 Use pip to get tools
			pip install flask
			pip install sqlalchemy
			pip install flask-admin

	* 12. ~~pip install sqlalchemy~~		* 8. Get our tools

	* 13. get rdalchemy.git		* 9. Get UCSF Software
			get rdalchemy.git

	* 14. pip install flask-admin		get AgAd demo and data from git

	* 15. ~~get AgAd demo~~ ~~and data from git~~		* 10. Global update of all software
			yum update

	= testing =		= testing =

Frodo: 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 ..."

2014-10-21T18:43:47Z

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 ..."

New page

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

* 3. Download Python 2.7 tarball

* 4. cat centos-packages | xargs yum install -y

* 5. yum update - global update of all software

* 6. install python
./python.sh path-to-python-tarball /opt/python

* 7. run install ez_setup.py setuptools to new python install

* 8. use ezinstall to add pip

* 9. yum install psql

* 10. get rdkit.

* 11. pip install flask

* 12. pip install sqlalchemy

* 13. get rdalchemy.git

* 14. pip install flask-admin

* 15. get AgAd demo and data from git

= testing =

* 1 . set up a web server

* 2. run DOCK

= optional set up =
* 1. queuing system

* 2. nfs server and central services

[[Category:Sysadmin]]