[Bioperl-pipeline] pipeline modifications
shawnh@fugu-sg.org
shawnh@fugu-sg.org
Fri, 13 Dec 2002 12:56:52 +0800 (SGT)
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
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