[BiO BB] Pipeline Tool

Ryan Golhar golharam at umdnj.edu
Tue Oct 6 16:47:08 EDT 2009

I create a program to do exactly this back in 2001 using Java.  Its a 
nice interface and worked well.  I wonder if I can upload it somewhere 
for public use.  Perhaps on bioinformatics.org?

Harry Mangalam wrote:
> 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..)
> http://www.vistrails.org/index.php/Main_Page
> hjm
> 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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