Install SEA: Difference between revisions

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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





Revision as of 20:49, 14 September 2012

This is intended for Shoichet lab setup. But we hope other find it useful.


The full SEA installation requires a few Python packages:

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

Users outside of the network should see the 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.




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 <<<<<<<<<<<<<<

  1. wd: ~bet/svn/

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

>>>>>>>>>>>>> Install <<<<<<<<<<<<<<

  1. wd: ~bet/svn/sea/trunk/

sudo ./setup.py install

  1. 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)
  1. wd: ~bet

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

  1. 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 <<<<<<<<<<<<<<

  1. 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