Install SEA - Revision history

Frodo at 06:42, 13 March 2014

2014-03-13T06:42:50Z

← Older revision		Revision as of 06:42, 13 March 2014
Line 70:		Line 70:
	[[Category:Off target effects]]		[[Category:Off target effects]]
	[[Category:Pharmacology]]		[[Category:Pharmacology]]
	[[Category:~~Install~~]]		[[Category:Sysadmin]]

Frodo at 05:23, 13 March 2014

2014-03-13T05:23:25Z

← Older revision		Revision as of 05:23, 13 March 2014
Line 68:		Line 68:

	[[Category:SEA]]		[[Category:SEA]]
	~~[[Category:Scaffold hopping]]~~
	[[Category:Off target effects]]		[[Category:Off target effects]]
	[[Category:Pharmacology]]		[[Category:Pharmacology]]
	[[Category:Install]]		[[Category:Install]]

Frodo at 20:02, 31 October 2013

2013-10-31T20:02:23Z

← Older revision		Revision as of 20:02, 31 October 2013
Line 71:		Line 71:
	[[Category:Off target effects]]		[[Category:Off target effects]]
	[[Category:Pharmacology]]		[[Category:Pharmacology]]
			[[Category:Install]]

Matthew O'Meara at 20:18, 29 October 2013

2013-10-29T20:18:54Z

← Older revision		Revision as of 20:18, 29 October 2013
Line 17:		Line 17:
	sudo rpm -Uvh epel-release-6-7.noarch.rpm		sudo rpm -Uvh epel-release-6-7.noarch.rpm
	yum update		yum update
	yum install scipy numpy numpy-f2py atlas atlas-devel mysql mysql-server		yum install scipy numpy numpy-f2py atlas atlas-devel mysql mysql-devel mysql-server

	The additional web-based results viewer requires:		The additional web-based results viewer requires:

Frodo at 23:15, 11 October 2012

2012-10-11T23:15:58Z

← Older revision		Revision as of 23:15, 11 October 2012
Line 52:		Line 52:
	>> SEA database login information		>> SEA database login information
	>> [scratch]		>> [scratch]
	>> host=scratch.~~compbio~~.~~ucsf.edu~~		>> host=scratch.bkslab.org
	>> user=your_username		>> user=your_username
	>> pass=your_password		>> pass=your_password

Therese: 13 revisions

2012-10-08T20:27:50Z

13 revisions

← Older revision

Revision as of 20:27, 8 October 2012

Tbalius at 21:11, 1 October 2012

2012-10-01T21:11:24Z

New page

This is intended for Shoichet lab setup. But we hope other find it useful. See [[SEA]]

The full SEA installation requires a few Python packages:

* [http://numpy.scipy.org/ NumPy]
* [http://scipy.org/ SciPy]
* [http://math-atlas.sourceforge.net/ ATLAS]

These are best installed using your distribution's package manager:

yum install scipy numpy atlas atlas-devel mysql mysql-server

On CentOS systems you may need to add an additional repository to make all of these packages available:

wget http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-7.noarch.rpm
sudo rpm -Uvh epel-release-6-7.noarch.rpm
yum update
yum install scipy numpy numpy-f2py atlas atlas-devel mysql mysql-server

The additional web-based results viewer requires:

* Apache
* PHP
* PHP MySQL Libraries

sudo yum install php php-mysql php-cli

You will need to checkout the most recent version of the SEA source code. From within the BKS network this can be done by:

svn co file:///raid4/svn/sea/trunk /tmp/sea
svn co file:///raid4/svn/sea.molecule/trunk /tmp/sea
svn co file:///raid4/svn/tanimoto/trunk /tmp/sea

Users outside of the network should see the [http://sea.bkslab.org/ SEA website] for source code availability.

Notes about checkout:

* If you will be installing SEA into the system's Python site-packages the source code will need to be checked out into a location with write access for both the active user account '''and''' the local root user, hence `/tmp/sea`.
* It is important that you are using the version of python into which you NumPy and SciPy have been added and which you intent to install SEA to. For example if you wish to install SEA to the local python instance `which python` should return `/usr/bin/python`. If it does not, the easiest way to remidy this is `alias python /usr/bin/python`. This can be the source of many headaches.

After checking out and installing these, you'll need to set up you public_html to view the SEA runs results on the web viewer (in your home directory):

mkdir public_html
cp -r /usr/arch/share/sea/www/ public_html/sea
cp ~keiser/.sea.cfg .
cp ~keiser/.sea_databases.cfg .
cp ~keiser/.sea_molecule* .
rm .sea_molecule.cfg

# Change .sea_databases.cfg file
>> SEA database login information
>> [scratch]
>> host=scratch.compbio.ucsf.edu
>> user=your_username
>> pass=your_password
>> db=your database

You will also need to create the MySQL database:
sea-database
create

The recommended database settings are in /etc/my.cnf

Note that there is a useful manunal distributed with the source code located in `${seapath}/sea/data/doc/manual.html`.

[[Category:SEA]]
[[Category:Scaffold hopping]]
[[Category:Off target effects]]
[[Category:Pharmacology]]

Tbalius at 20:49, 14 September 2012

2012-09-14T20:49:55Z

← Older revision		Revision as of 20:49, 14 September 2012
Line 44:		Line 44:

	Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`.		Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`.

			Here is the text from SEA_setup.txt:

			>>>>>>>>>>>>> Export svn project <<<<<<<<<<<<<<
			# wd: ~bet/svn/
			svn co file:///raid4/svn/sea
			svn co file:///raid4/svn/sea.molecule
			svn co file:///raid4/svn/tanimoto

			>>>>>>>>>>>>> Install <<<<<<<<<<<<<<
			# wd: ~bet/svn/sea/trunk/
			sudo ./setup.py install

			# wd: ~bet/svn/sea.molecule/trunk/
			./setup.py build
			sudo ./setup.py install
			Warning: Package missing: daylight
			>> It just notices that daylight isn't available on your local machine (which is fine because we only have a daylight license for korn)

			# wd: ~bet
			mkdir public_html
			cp -r /usr/arch/share/sea/www/ public_html/sea
			cp ~keiser/.sea.cfg .
			cp ~keiser/.sea_databases.cfg .
			# Change config file
			>> SEA database login information
			>> [scratch]
			>> host=scratch.compbio.ucsf.edu
			>> user=bet
			>> pass=rubberducky
			>> db=bet_sea

			cp ~keiser/.sea_molecule* .
			rm .sea_molecule.cfg
			python /usr/arch/bin/sea-database

			>>>>>>>>>>>>> Create database <<<<<<<<<<<<<<
			# wd: ~bet
			sea-database
			create

			>>>>>>>>>>>>> Optimize MySQL settings <<<<<<<<<<<<<<
			Recommended settings in: /etc/my.cnf

			mysql -ubet -p bet_sea -hscratch.compbio.ucsf.edu

			>>>>>>>>>>>>>> User manual <<<<<<<<<<<<<<<<
			~bet/svn/sea/trunk/data/doc/manual.html

Tbalius at 20:47, 30 August 2012

2012-08-30T20:47:35Z

← Older revision		Revision as of 20:47, 30 August 2012
Line 35:		Line 35:
	Notes about checkout:		Notes about checkout:

	* If you will be installing SEA into the system's Python site-packages the source code will need to be checked out into a location with write access for both the active user account and the local root user, hence `/tmp/sea`.		* If you will be installing SEA into the system's Python site-packages the source code will need to be checked out into a location with write access for both the active user account '''and''' the local root user, hence `/tmp/sea`.
	* It is important that you are using the version of python into which you NumPy and SciPy have been added and which you intent to install SEA to. For example if you wish to install SEA to the local python instance `which python` should return `/usr/bin/python`. If it does not, the easiest way to remidy this is `alias python /usr/bin/python`. This can be the source of many headaches.		* It is important that you are using the version of python into which you NumPy and SciPy have been added and which you intent to install SEA to. For example if you wish to install SEA to the local python instance `which python` should return `/usr/bin/python`. If it does not, the easiest way to remidy this is `alias python /usr/bin/python`. This can be the source of many headaches.






	Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`.		Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`.

Tbalius at 20:25, 30 August 2012

2012-08-30T20:25:08Z

← Older revision		Revision as of 20:25, 30 August 2012
Line 8:		Line 8:
	* [http://math-atlas.sourceforge.net/ ATLAS]		* [http://math-atlas.sourceforge.net/ ATLAS]

	These are best installed using ~~your~~ your distribution's package manager:		These are best installed using your distribution's package manager:

	yum install scipy numpy atlas atlas-devel mysql mysql-server		yum install scipy numpy atlas atlas-devel mysql mysql-server