[Bioperl-l] bioperl installation

Brian Osborne brian_osborne at cognia.com
Thu Jul 22 12:01:18 EDT 2004


The section in the on-line instruction, the INSTALL page, talking about
installing in a personal area using CPAN is called "INSTALLING BIOPERL IN A

You can also use CPAN to install accessory modules in your
local directory. First enter the CPAN shell, then set the
arguments for the command "perl Makefile.PL", like this:

>perl -e shell -MCPAN
cpan>o conf makepl_arg LIB=/home/users/dag/My_Local_Perl_Modules

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Xiang Deng
Sent: Thursday, July 22, 2004 11:42 AM
To: Jason Stajich
Cc: bioperl-l-bounces at portal.open-bio.org; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] bioperl installation

Thanks for your message, Jason.

The problem is I don't have permission to install bioperl into the
standard site_perl/system area. From the on-line instruction at
bioperl.org the only way I can get it installed is to use "make", not

So could you please let me know where I can download Inline::MakeMaker and
Inline::C module. Everything I downloaded is from bioperl.org. I did not
see where I can get these two. And if I get it which directory I should
put them in.



Department of Pharmacology and Cancer Biology
Duke University Medical Center
Durham, NC 27710
Phone: 919-4792339

Jason Stajich <jason at cgt.duhs.duke.edu>
Sent by: bioperl-l-bounces at portal.open-bio.org
07/22/2004 11:25 AM

Xiang Deng <xiang.deng at duke.edu>
bioperl-l at bioperl.org
Re: [Bioperl-l] bioperl installation

Did you install Inline::C?
>From the README in bioperl-ext directory
  o Installing

 Depending on your choise of extensions, you might need
 Inline::MakeMaker and Inline::C to create the makefile. Use for
 example the cpan program to install Inline::MakeMaker and answer yes
 when prompted to install Inline::C.

This line gives you a hint:
> Can't locate Inline/MakeMaker.pm in @INC (@INC contains:

Did you also install the staden library?
On Thu, 22 Jul 2004, Xiang Deng wrote:

> To whom it may concern,
> I am trying to install bioperl locally under my peronal folder. The core
> modules were successfully installed. I ran through a simple perl script
> use bio::perl or bio::seq without complain. but I got problem with
> installing bioperl-ext-1.4.
> When I installed core modules I used this
> >perl Makefile.PL LIB=/my_local_directory/
> My first question is whether or not I have to use the same way to deal
> with ext modules too and I can use the same directory or a separate one.
> Actually I tried both and both failed with error message as follows:
> mendel 207% perl Makefile.PL
> Checking if your kit is complete...
> Looks good
> Writing Makefile for Bio::Ext::Align
> ERROR from evaluation of
> Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.6.1/IP27-irix /usr/local/lib/perl5/5.6.1
> /usr/local/lib/perl5/site_perl/5.6.1/IP27-irix
> /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl
> /v0/users/deng0007/my_bioperl/bioperl-ext-1.4 .) at ./Makefile.PL line
> BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> could you please let me know what I did wrong or miss in there? thanks a
> lot,
> Xiang
> Department of Pharmacology and Cancer Biology
> Duke University Medical Center
> Durham, NC 27710
> Phone: 919-4792339

Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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