Hello Matt, Thanks a lot for your answer.
So, I was already executing BLAST using External Execution actor. But I'd like to have a 'blast' actor that receives through ports the blast inputs (database and input sequences). I've tried to customize the External Execution actor adding a 'inputsequences' port, but I think this should be a PortParameter type, so I can read it inside a parameter and put it in the command line, so I'd have: - a PortParameter called 'inputsequences' - a Parameter called 'inputsequences' - and the command would be: blastall -i $inputsequences Would this work? I don't figure out how to add a PortParameter using 'configure ports' option. Just some other doubts if you can help: 1- If I customize External Exec actor this way, how could I transform it into another independent actor, with a new lsid? 2- I've made some changes in the actor and I've exported it as .kar. How do I use this 'new' actor in other workflows? 3- Does this 'new' actor created in item 2 continue using the external exec class, or is it loaded and called only using the moml exported? 4- How do I 'edit' an actor changing directly its code (java or moml?) ?? Thanks a lot, Luciana > Hi Luciana, > > On Thu, Feb 24, 2011 at 10:47 AM, Luciana Gomes > <lgomes at inf.puc-rio.br>wrote: > >> Hello, >> >> do you have some example of an actor that encapsulates a command-line >> tool, like BLAST tool? >> > There are two examples of using the External Execution actor to execute an > external program and return the results. See the Getting Started Guide > examples. Example 07 shows how to run a java HelloWorld program, and > example 08 shows how to run the R system. Either demo could be easily > adapted to run the Blast tool. You can find the demos in your KeplerData > folder in your home directory: > > KeplerData/workflows/module/outreach-2.1.0/demos/getting-started/07-CommandLine_1.xml > > KeplerData/workflows/module/outreach-2.1.0/demos/getting-started/08-CommandLine_2.xml > > >> Is it possible to make this kind of actor outputs a file, which is for >> example the alignment file generated by BLAST, considering this can be a >> big file? >> > The external execution actor will pass along anything that comes out of > STDOUT to the output port of the actor. If you are concerned about file > size, the easiest thing to do would be to arrange for your commandline > tool > to output a filename that is processed downstream by other actors as > needed. > > >> Would this file be stored in DATA table of provenance database? >> > The provenance DB captures port outputs, so as far as I know it would be > stored if provenance is on. > > Matt > >> >> Thanks a lot, >> -- >> Luciana >> >> >> >> >> >> _______________________________________________ >> Kepler-users mailing list >> Kepler-users at kepler-project.org >> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users >> > --
