[BiO BB] Pipeline Tool

Harry Mangalam harry.mangalam at uci.edu
Tue Oct 6 16:28:33 EDT 2009

There's a very expensive commercial tool called Scitegic's Pipeline Pilot (may 
be been re-ingested by Accelerys).  It's very well-designed (and should be 
for the price), but it runs only on MS Windows (tho some back end stuff may 
now run on *nix).

However, you could do a lot worse than try VisTrails.  A supported Open Source 
PyQt-based visual workflow, it's meant to be easy to install (especially on 
Linux) and very easy to use & debug.  It's an ongoing project and the 
developers are very responsive and have one of the best senses of how to 
implement a UI of the OSS ones I've seen/used.  It also tracks the changes of 
the workflow in a very subversion-like way (the 'trails' part of it).  It 
balances ease of use with power in ways that others have not seen fit to do 
(see Kepler - enormously powerful, unusably complicated IMHO..)



On Tuesday 06 October 2009 06:32:24 Daniel Xavier de Sousa wrote:
> Hi Everybody,
> I'm looking for a tool for run Genome Project. In other words, I want a
> system web to submit chromatogram, and process on it bases calling (PHRED),
> vector cleaning  (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) -
> PIPELINE. And I would like to see all data on graphic interface.
> I have tried many others tools, as ESTWeb. But all them have different
> problems: the project has finished, there is not support, there is no lab
> using,...
> I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because
> I would like to get some one that there are labs using it.
> No matter if the tool is comercial (have to pay for it). I really want
> resolve my problem of pipeline process.
> Can anyone, suggest one?
> Thanks,
> -Daniel Xavier de Sousa
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Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine
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