Install SEA

From DISI
Revision as of 20:20, 30 August 2012 by Tbalius (talk | contribs)
Jump to navigation Jump to search

This is indened 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 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 availibility.

Notes aboute 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`.