Failing to install BioPerl on Windows

biohisham has asked for the wisdom of the Perl Monks concerning the following question:

I've been trying to install BioPerl, I tried so using ppm and ppm gui for my Windoze XP and Active Perl 5.10, I have been failing terribly even though I am following the directions from BioPerl official site and having read the instructions carefully, I don't know where I am falling behind. When I type,

ppm>search BioPerl
[download]

I get only one search result, which is

Bundle-BioPerl
A bundle to install external CPAN modules used by BioPerl 1.5.2
Version 2.1.8
Provide: Bundle::BioPerl ...etc
[download]

which I understood as: BioPerl is not available on the ppm cpan this way. That made me go and download the zip file BioPerl-1.6.0.zip from http://bioperl.org/DIST/ and extract it to a directory location , now trying to

> ppm install path-to-BioPerl-1.6.0           #from the DOS prompt
#or
> ppm install path-to-BioPerl-1.6.0.ppd

#I get the following errors, respectively: 
ppm install failed: Can't find any package that provides BioPerl-1.6.0
ppm install failed: 404 file does not exist
[download]

I also tried to look for the nmake.exe utility in case I downloaded the gz version of BioPerl but I am finding it too difficult for me to follow (confusing and don't seem to address the issues from the beginning).

Is there a known compatibility hitches between BioPerl and the version of Perl I am using?, can anyone graciously provide guidance on how to effectively download this module?

Thanking you all

Significant update: I got successful finally and installed it, in my search around there were reported incompatibility but this seems to have been resolved and I got bioperl downloaded with 90 modules, yet to check and test however. Here is the link to the website I got the tips from http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows, in figuring out the repository all you have to do is just copy paste the name and location from the table of repositories to the respective place in the PPM gui widget, then after that proceed with the installation.

Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.

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Re: Failing to install BioPerl on Windows by Khen1950fx (Canon) on Sep 24, 2009 at 01:31 UTC
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]	[reply] [d/l]
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]
Re: Failing to install BioPerl on Windows by Bloodnok (Vicar) on Sep 24, 2009 at 09:13 UTC
I appreciate that struggling is all part of the learning process, but ever since I was shown Strawberry Perl (by another monk), I've not used anything else on Windoze - it's an effortless installation and life's too short to be wrestling, seemingly endlessly, with Windoze and its foibles & peculiarities - despite Dave Roths' excellent Windoze orientated books and website. A user level that continues to overstate my experience :-))	[reply]
Re^2: Failing to install BioPerl on Windows by biohisham (Priest) on Sep 24, 2009 at 11:17 UTC
It was despair for a while, it's been a week that I'm trying. Strawberry Perl is popular indeed, by chance I downloaded it first but I faced issues with it and ended up downloading the Active State's, but this's not in anyways bearing discredit to Strawberry Perl nor its stability. Windoze presents unexpected (unaccepted) behavior all the times, imagine, my first shot with BioPerl was to do exactly what I've done today, install the repositories and search for the Module, and it gave me failures, so over the course of the week I tried other strategies none of which worked, and after having posted my question, I went back to what I tried a week ago and this time it decided to work!!!, back then I typed the URLs in, today I just pasted them as shortcuts to where they're supposed to. A blind shot in the darkness sort of. one big challenge remains however, I seek direction down the road of finding stronger BioPerl tutorials that address the various Bioinformatics issues down to their core, with examples and case studies, I appreciate help and your replies to this node, all of you, can potentially serve a lot of people facing similar struggles. Soliciting council is Wisdom. Thanks... Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.	[reply] [d/l]
Re^3: Failing to install BioPerl on Windows by addinall (Novice) on Feb 07, 2010 at 06:34 UTC
one big challenge remains however, I seek direction down the road of finding stronger BioPerl tutorials that address the various Bioinformatics issues down to their core, with examples and case studies, I appreciate help and your replies to this node, all of you, can potentially serve a lot of people facing similar struggles. Soliciting council is Wisdom. I too am using BioPerl on Windoze all on my own. So whether I am doing it correctly or not, who knows.... I would dearly love to find some "OK, here is how it should be done" tutorials, esp. if it targets Windows. I can read the *NIX stuff OK, but I don't know how to make a lot of it work in XP. Mucho Thanks, Mark.	[reply]