This is a fork of galaxy-central for working on some new NGS wrappers - Picard and GATK in particular.
Ross Lazarus wrote most of the original tool wrappers and Raphael Lullis got all the tests working and cleaned the code up removing the most ugly hacks and rationalizing the redundant material Ross threw over the wall.
Look for GATK and Picard in the tool names in tools/rgenetics of this clone.
Check out Brad's pipeline picard code git clone https://github.com/chapmanb/bcbb.git eg https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/automated_initial_analysis.py
Much neater. Could retain the xml wrappers here but call code based on that fork.
Notes as at January 6 2011
Yes, progress has been made, but in my hands, Picard is still too fussy to be reliable in the wild IMHO.
Brad has no (need for) xml - I have xml forms for a bunch of useful Picard procedures, with loc files and working tests, but with far less elegant python code. I prefer his code to mine where it does the same thing. The rgGATKrecalibrate tool does some magic and lays out thumbnails of all the QC pdfs as pre and post in columns - users love it..
Suggestion: If you had time, Brad's code could be harnessed and run using my existing tool forms, for all the existing tools. Most of the functions will kind of fit.
Even after I filter all the bad stuff I can, I'm still seeing Picard java tracebacks from what looks like reasonable real data far too often for me to be happy. Same goes for GATK tools.
At this time, I'm sure they'll occasionally and unpredicably fail with real world crappy data in ways that I can't easily fix. I'll build up a library of data that seems problematic as I find it so we can stress test any improved wrapper code?
Notes As at December 10
These tools are very much pre-beta - feel free to test them out but expect road bumps.
jars and R scripts are included here although they would not be in a normal distribution.
tool_conf.xml.rgenetics contains the new NGS tools.