[Bioperl-l] help on Bio-Perl Installation

Mark Johnson johnsonm at gmail.com
Tue Nov 11 15:19:19 EST 2008

On Fri, Oct 24, 2008 at 12:06 PM, Jie Zhang <jieuiuc at yahoo.com> wrote:
> HI,
> I'm new to BioPerl and just finished installing BioPerl on Windows XP by dowloading and unpack the file bioperl-1.5.2_102.tar.gz  from the Bioperl.org website, then strictly followed the
>manual installation instruction. All the Build and Test steps were fine although there were some unimportant modules failed to install. I was able to view the documentation by typing >perldoc Bio::Perl in the command window. However, when I tested if it is installed properly, I encountered problem. I wrote a two-line script file called bp.pl
> #!/bin/perl -w
> use Bio::Perl;
> The compilation step failed and gave me this message"use not allowed in the expression at bp.pl line 3, syntax error at bp.pl line 3, near"use Bio::Perl"...."
> That warning appeared no matter the script is "use Bio::Seq" or other modules. It seems use is not allowed here. What could be wrong during installation? Could you please help me?
> Thank you very much
> Jie

    What distribution of Perl are you using?  ActiveState?
Strawberry?  How are you invoking your script?  A Unix style shebang
(#!/path/to/interpreter) probably won't work without some deep magic,
and perhaps not even then.  If you have perl in your path, try 'perl
bp.pl', if you haven't already.

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