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

[Gert Thijs]

Julio,

As far as I understand the problem from your description, I guess the
problem stems from the way java runs system calls. We had a similar
problem here a while ago. I do not remember the details of the
problem/solution, but I remember that part of the problems was that some
SHELL variables are not the same in the java system call compared to
running it on the command line. If I am not mistaken, I think that you
can add extra arguments to the java system call to set these shell
variables like PATH, PERL5LIB. 

Gert
 

On Mon, 2004-03-22 at 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
> 
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-- 
+ Gert Thijs          
+ Postdoctoral Researcher
+  K.U.Leuven
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