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

Andreas Kahari ak at ebi.ac.uk
Mon Mar 22 04:31:12 EST 2004

On Mon, Mar 22, 2004 at 10:08:21AM +0100, 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

Do you get any error messages whatsoever?

(Is there a reason you don't want to use BioJava for the whole
application?  It should be able to handle blast parsing I would
have thougth.)


|[][]|      Andreas Kähäri                                |=][=|
| [] |      EMBL, European Bioinformatics Institute       |[==]|
|[][]|      Wellcome Trust Genome Campus                  |=][=|
| [] |      Hinxton, Cambridgeshire, CB10 1SD             |[==]|
|[][]|      United Kingdom                                |=][=|

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