[Bioperl-pipeline] pipeline modifications

[shawnh@fugu-sg.org]

Hi folks,
You might have noticed a flurry of commits last nite and for those
who have updated, you might find what you have been using might not be working!
So I want to update a little what I did.

First the Changes:

I have split the parameters column in the analysis table into 2 columns:

	1)analysis_parameters 
	2)runnable_parameters

Analysis parameters are parameters specfic to the wrapper or binary.
So to use this blast example, these would be the options like -p blastp -e 1e-05 etc

Runnable parameters are params that are specific to the runnable.
This could be stuff like result directory in which to store files etc.

This separation makes things a little clearer when writing xml.


Ramifications of the change:

xml files: I have updated most of the xml files to reflect the changes including
           the Xml2DB script,
           so pls work with those, or modify yours by replacing
           <parameters> with <analysis_parameters> or <runnable_parameters> 

code     : A bunch of changes everywhere.
	   AnalysisAdaptor,Analysis objects obviously
	   All the runnables to read from the runnable_parameters method.
	   I also modified the runnable so that they set the program_file path if 
           provided properly by using the $wrapper->executable method.

obviously I may have missed out something or other in the process, but I will look
into writing more rigorous pipeline tests.
 
The other change that I want to highlight is I have moved setup_file_blast.pm
into setup_file.pm. I haven't removed setup_file_blast but will make it deprecated
soon once more testing is done.

Previously setup_file_blast was a specific 
input create module that takes file contain a bunch of sequences and setups it
up for blasting in the pipeline.

Now, setup_file is a more generalized one that aims to setup any file based analysis 
which allow different file formats to be read and written.
So far, I have managed to run clustalw and dba and blast,will be working on protdist and 
the other phylip ones soon.


cheers,

shawn




-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************