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

Gert Thijs gert.thijs at esat.kuleuven.ac.be
Mon Mar 22 05:06:04 EST 2004


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. 


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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
+ Gert Thijs          
+ Postdoctoral Researcher
+  K.U.Leuven
+  Kasteelpark Arenberg 10 
+  B-3001 Leuven-Heverlee  
+  Belgium  
+ Tel  : +32 16 327928 
+ Fax  : +32 16 321970
+ email: gert.thijs at esat.kuleuven.ac.be 
+  http://www.esat.kuleuven.ac.be/~thijs
+  http://www.esat.kuleuven.ac.be/~dna/BioI/

More information about the Bioperl-l mailing list