liv has asked for the wisdom of the Perl Monks concerning the following question:

Hi all, I'm trying to run a program using perl script, I started with the data in the tutorial: C:\Users\user\Desktop\cgview\cgview_xml_builder>perl cgview_xml_builder.pl -sequ ence sample_input/R_denitrificans.gbk -output R_denitrificans.xml -tick_density 0.7java -jar -Xmx1500m Somehow It couldn't work, I'm getting the error as: Can't locate Bio/SeqIO.pm in @INC (@INC contains: C:/Perl/site/lib C:/Perl/lib . ) at cgview_xml_builder.pl line 8. BEGIN failed--compilation aborted at cgview_xml_builder.pl line 8. I have installed ActivePerl. This is my first time using perl, anyone can enlighten me? Thanks!
  • Comment on Can't locate Bio/SeqIO.pm in @INC with ActivePerl installed

Replies are listed 'Best First'.
Re: Can't locate Bio/SeqIO.pm in @INC with ActivePerl installed
by Anonymous Monk on Sep 16, 2011 at 06:36 UTC
[reply]
Re: Can't locate Bio/SeqIO.pm in @INC with ActivePerl installed
by Khen1950fx (Canon) on Sep 16, 2011 at 07:06 UTC
    BioPerl doesn't come with ActivePerl, so it's not installed. Here's a little install script that'll do it for you: 
    #!/usr/bin/perl

use strict;
use warnings;
use CPAN;

CPAN::Shell->install(

"Bundle::BioPerl",
"Bio::Seq",
"Bio::SeqIO::staden::read",
"Bio::Factory::EMBOSS",
"Bio::Tk::SeqCanvas",
"Bio::DB::Annotation");

    [download]
    There will be a bunch of test failures, so be prepared to spend some time working it. A good way to learn BioPerl:).

    Update: Here's a newer version. Note that BioPerl::DB requires BioSQL. Install that before you run the script. 

    #!/usr/bin/perl

use strict;
use warnings;
use CPAN;

CPAN::Shell->force(qw(
install 
Bundle::BioPerl
Bio::DB::ESoap
CJFIELDS/BioPerl-Network-1.006900.tar.gz
CJFIELDS/BioPerl-DB-1.006900.tar.gz));

    [download]
[reply]
[d/l]
[select]
[reply]

Back to Seekers of Perl Wisdom