[Bioperl-l] Is this a bug?
sallyli97 at yahoo.com
Sat Jun 21 13:26:07 EDT 2003
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
Can't exec "/home/bioperl/clustalw1.82/clustalw": Too
many open files at
------------- EXCEPTION -------------
MSG: Clustalw call
-outfile=/tmp/gLz1itml6n) crashed: 65280
--- Juguang Xiao <juguang at tll.org.sg> wrote:
> >> Hi, there,
> >> I would like to know how to call bioperl method
> >> 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 Xiao
> Temasek Life Sciences Laboratory, National
> University of Singapore
> 1 Research Link, Singapore 117604
> juguang at tll.org.sg
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