[Bioperl-l] Help installing BioPerl
popgen23 at mac.com
Mon Sep 13 13:47:32 EDT 2004
I'd rather not add lines to my scripts because I distribute them among
colleagues and it would be a pain to alter them every time a make a
script. Well, being that I am still new to BioPerl and Perl in general,
I do not have any experience in manipulating this PERL5LIB variable or
how to do that. I have re-ran the CPAN-based install 4 times to no
avail (as root even). How do I find a location that is known to PERL
and where do I find this INSTALL file?
Hmm, seems like I should just write things from scratch rather than use
BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather try
installing/using BioPerl :-)
Sorry, about this but I am trying to learn. I am trying to follow along
with the "perl for bioinformatics" books but they are of no use when it
comes to trouble shooting bio::perl.
On Sep 13, 2004, at 11:22 AM, Brian Osborne wrote:
> One fix is to put a "use lib <Bioperl home directory>;" line into your
> scripts, another fix is to set the PERL5LIB variable to the Bioperl
> directory, a third fix is to do the CPAN-based install again but set
> installation directory to a location known to Perl (see the INSTALL
> file for
> the specific CPAN command).
> 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 Michael
> Sent: Monday, September 13, 2004 12:59 PM
> To: Brian Osborne
> Cc: bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] Help installing BioPerl
> In a sense , yes.
> When I try to run any script using Bio::Perl I get this error:
> "Can't locate Bio/Perl.pm in @INC".
> On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote:
>> Do you mean that the test for Bio::Perl is failing?
>> 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 Michael S.
>> Robeson II
>> Sent: Sunday, September 12, 2004 12:16 PM
>> To: bioperl-l at portal.open-bio.org
>> Subject: [Bioperl-l] Help installing BioPerl
>> I have successfully installed BioPerl on several machines running Mac
>> OS X (10.3.5) w/o any trouble. However one of my machines (same OS)
>> install is not working. Basically I keep getting "Error 2" problems at
>> the end of an install.
>> I've used the "perl -MCPAN -eshell" as both a normal user and root and
>> it still does not work. I've tried this while installing the
>> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz".
>> Basically what it amounts to is that I get an error that says "Can't
>> locate Bio/Perl.pm in @INC". I basically know what this means but I am
>> not so sure how to fix this or what to do.
>> Any help would be greatly appreciated.
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
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