Re: Failing to install BioPerl on Windows

Here's a little script that I use for a fresh install of BioPerl. It works on macosx, Win32, and Linux. Don't let its small size throw you because it takes a long time:-).

#!/usr/bin/perl

use strict;
use warnings;
use CPAN;

CPAN::Shell->force('install',

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

Comment on Re: Failing to install BioPerl on Windows Download Code

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Re^2: Failing to install BioPerl on Windows by Corion (Patriarch) on Sep 24, 2009 at 07:00 UTC
Is the call to `->force` strictly necessary, or could you just use `->install` instead? I prefer to trigger the `->force` myself, after I've convinced myself that the test failures don't apply to my situation...	[reply] [d/l] [select]
Re^3: Failing to install BioPerl on Windows by Khen1950fx (Canon) on Sep 24, 2009 at 08:24 UTC
The call to force isn't strictly necessary. In my case, I was getting a few too many failures, so I just forced it to save some time. BioPerl works well for me otherwise. Thanks for pointing it out.	[reply]
Re^2: Failing to install BioPerl on Windows by biohisham (Priest) on Sep 24, 2009 at 10:41 UTC
If only I found your script earlier when I first posted my dilemma to SOPW, but hey, this is like one great way to keep being lazy, I have this question though, if I installed Bundle::BioPerl(as in `Cpan::Shell->force('install',"Bundle::BioPerl");`) and then went on to install the BioPerl module itself, or let's say if I installed BioPerl module directly first hands without installing the other modules would it not be sufficient? I mean, I don't want to remember all the dependencies names of the BioPerl module and further still I don't want to write them one by one in the list of the Cpan::Shell->force(); Thanks a million :) Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.	[reply] [d/l] [select]