[Bioperl-l] Is this a bug?

[Sally Li]

Hi, there,

Thanks for the information about java<=>perl. I may
have to work from scratch using perl api for c and
then use jni to call c methods if it is really needed.


Here is the another problem I have. I wonder if it is
a bug?

Can't exec "/home/bioperl/clustalw1.82/clustalw": Too
many open files at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/Clustalw.pm
line 580.

------------- EXCEPTION  -------------
MSG: Clustalw call
(/home/bioperl/clustalw1.82/clustalw align
-infile=test.fasta -output=gcg  
-outfile=/tmp/gLz1itml6n) crashed: 65280



Thanks!

Sally

--- Juguang Xiao <juguang at tll.org.sg> wrote:
> >
> >> Hi, there,
> >>
> >> I would like to know how to call bioperl method
> from
> >> java. Any idea will be appreciated.
> 
> 
> Do you want to pass objects or borrow functions from
> bioperl? This is 
> too computer issue. A year ago, ensembl tried to
> solve the similar 
> problem to top up ensembl-java usage and popularity,
> with no sounding 
> result. I was working on it.
> 
> Actually we do not need to solve the problem on
> bioperl level.  
> Methologically, you can pass the objects in file
> way, and compose a 
> (perl/bash) script to assembly up the process
> written in bioperl and 
> java. Or simple use bash's pipe
> 
> cmd1 | cmd2
> Pipe; use output from cmd1 as input to cmd2.
> 
> Hope this tip help.
> my  S$0.002
> 
> Juguang
>   ------------ATGCCGAGCTTNNNNCT--------------
> Juguang Xiao
> Temasek Life Sciences Laboratory, National
> University of Singapore
> 1 Research Link,  Singapore 117604
> juguang at tll.org.sg
> 


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