[Bioperl-l] Can't run bioperl from java

mpjfb at usc.es mpjfb at usc.es
Mon Mar 22 06:08:40 EST 2004

Thanks for your fast answers.
I tryied both writting the commands in a single string and in an array and in
both cases I have he same problem.
I'm not getting any error message. What it happens is that the perl scripts
starts and when it comes to analize the first sequence it seems that the perl
script ends and the java programs goes to the next task as if everything went
well. Maybe the problem is not with bioperl but with the programs bioperl calls
(blast in this case) as the program finishes working when it's supposed to start
with the first blast.
I check both the console and the java error log and there are no error messages
in any of them.
I will try to test a bioperl script were I don't call any other external program
like blast to check if this is the problem.

Thanks again, Julio.

Mensaje citado por Oliver Wafzig <Oliver.Wafzig at axaron.com>:

> Hi Julio,
> if you are using one string (containing all your perl commandline args and 
> whitespaces) to call 'runtime().exec()', try it using a string array. 
> It might help.
> Oliver
> On Monday 22 March 2004 10:08, mpjfb at usc.es wrote:
> > Hello.
> > I don't know if this is of topic but I have some problems trying to run
> > Bioperl from Java.
> > My problem comes as follows:
> > I wrote a perl script tha perform multiple blast alignments and parses
> > them. As this programs needs to be run in text mode (and it can be really
> > painfull when you have to add many arguments) I decided to write a GUI
> > using JAVA. When I run my perl script directly it works fine and if I run
> > other perl scripts (that don't use bioperl) from the GUI everything works
> > fine.
> > Does anyone have any advice of what can be the problem???? I thought that
> > it can be some error with my bioperl install (I move from OSX 10.1 to
> > 10.3). Any help would be apprecited.
> > thanks a lot, Julio
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l

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