[Bioperl-l] bioperl-ext package installation error

Alan Twaddle twaddlac at gmail.com
Fri Nov 19 15:03:14 EST 2010

Hello all,

     I am trying to write a simple script to parse an ABI file into usable
data which requires the staden io_lib of which I installed. However, am
receiving an error message when trying to run my script that says the
------------- EXCEPTION: Bio::Root::SystemException -------------
MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
package has been installed successfully!
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
STACK: AB1_parser.pl:10

I didn't receive any error messages when installing the staden package so
I'm assuming that there's some path specified in some file that is pointing
to the wrong place. I don't know if this is the case but if you have any
suggestions about how to fix this I would greatly appreciate it! Thank you
very much!


Alan Twaddle, B.S.
MUC class of 2010

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