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

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Re: Can't locate Bio/SeqIO.pm in @INC with ActivePerl installed
by Anonymous Monk on Sep 16, 2011 at 06:36 UTC
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");
    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));