Dependencies
============

Required
---------

- Python (>= 2.4)

- easy_install and setuptools for Python: probably your Linux/BSD/whatever 
  distribution already contains those pre-packaged. Otherwise, download
  ez_setup from http://peak.telecommunity.com/dist/ez_setup.py and run
  "sudo python ez_setup.py" which will install setuptools. For further
  details, visit
  http://peak.telecommunity.com/DevCenter/EasyInstall#installation-instructions 

- You will need several Python packages. Most installations include many
  or most of them. Just in case, from a fresh python installation (or if
  you use workingenv) you'll need to do:
      easy_install Pylons cheetah
      easy_install Paste
      easy_install PasteScript
      easy_install PasteDeploy
      easy_install Beaker
      easy_install nose
      easy_install WebHelpers
      easy_install simplejson
      easy_install FormEncode
      easy_install Myghty
      easy_install MyghtyUtils
      easy_install Routes

  see the script "install.in.workingenv.sh" which gives a possible script
  that will take care of installing a fresh, "isolated" working
  environment with workingenv, and will install all required Python
  modules (and will also install Asterias, and ask you to configure it.)


- LAM/MPI. Needed for the parallel computing. Get it from
  http://www.lam-mpi.org/, although your Linux distribution is likely to
  have LAM/MPI packages/binaries (in Debian you need lam-runtime, lam4-dev
  and lam4c2 or equivalent ---the shared libraries). [We will eventually
  move to Open MPI, but lots of our code depends on lamboot/lamhalt
  created/destroyed universes, and analogous commands are not yet
  available for Open MPI].

- R (>= 2.4.0), available from CRAN (http://cran.r-project.org ), and
  several R packages (available from CRAN) and BioConductor packages
  (available from http://www.bioconductor.org ). The required R/BioC
  packages are, right now: 'cgh', 'aCGH', 'cghMCR', 'DNAcopy', 'papply',
  'GDD', 'imagemap', 'waveslim', 'cluster', 'ADaCGH'. 
  

 

Optional but convenient
------------------------

- Virtual Python
  (http://peak.telecommunity.com/DevCenter/EasyInstall#creating-a-virtual-python )
  or workingenv (http://cheeseshop.python.org/pypi/workingenv.py/0.2 ) so
  as to install as non-root. 



Creating the egg 
================

ONLY if you downloaded the sources and want to create your own egg for
distribution, etc. NOT NEEDED if you have the egg or are using
easy_install directly to get the package from Cheese Shop!!!

If you downloaded the sources, go to the upper directory and do:

   python setup.py bdist_egg




Installation and Setup
======================

Install ``asterias`` using easy_install::

    easy_install asterias

It is better to install as non-root; among other things, the installation
process creates a bunch of tmp directories where files get written and
deleted from by the web server user. See workingenv or VirtualPython
options above.



Pylons
------

Make a config file as follows (execute, for instance, from the home of the
user you are installing for)::

    paster make-config asterias config.ini
    
Tweak the config file as appropriate and then setup the applicaiton::

    paster setup-app config.ini
    
Then you are ready to go.



The rest
--------

Go to the place where asterias is installed and enter the asterias
directory. Edit the file asterias_config2.ini. 

If the file asterias_config2.py is not executable, make it so
(e.g., chmod u+x asterias_config2.py). Now run it (./asterias_config2.py).




Other processes you might want to keep running
===============================================

lib/mpi_log/delete_old_dirs.py
------------------------------

If you have a cron job call this script periodically, your CGIs will have
to do less work, and will be faster. This is specially important in large
clusters or for applications that are only used sporadically, so that a
lot of old stuff can pile up.



lib/mpi_log/checkMPIdaemon.py
-----------------------------

We run this script every minute or so as a daemon that gets started when
the controlling machine(s) is booted. However you run or call it, this
daemon will prevent LAM/MPI from attempting to run in nodes that are not
functional. As well, if you use the appropriate code for having an email
(SMS, smoke sign, whatever) sent to you, you'll be notified when things
break. (E.g.: checking a machine is up via pings is not enough if the
file system is remounted read-only).

We use Debian, and have the following script linked from
/etc/init.d/checkMPIup


########################################################
#!/usr/bin/python

import os
import sys

start_stop = sys.argv[1]

if start_stop == 'start':
    tmp = os.system('/http/mpi.defs/local_checkMPIdaemon.py ')
    print 'OK'
elif start_stop == 'stop':
    tmp = os.popen('killall local_checkMPIdaemon.py')
    print 'OK'
elif start_stop == 'status':
    tmp = os.popen('ps -C local_checkMPIdaemon.py --no-headers').readline()
    if tmp:
        print 'OK, is running'
    else:
        print 'stopped'

############################################
where local_checkMPIdaemon.py is a local version of checkMPIdaemon.py,
with code for sending email, etc, etc.