[Bioperl-l] help!

Chris Fields cjfields at illinois.edu
Tue Feb 7 16:02:50 EST 2012


I guess one key question is where these CPAN installation instructions 
come from.  They're a bit odd, and if this is from the wiki we need to 
do some updating.

Re: local::lib, the docs on CPAN are pretty nice if one wants to use a 
single perl version.

https://metacpan.org/module/local::lib#The-bootstrapping-technique

In my case I use perlbrew (which is all local by default, and allows 
switching between perl versions).  Highly recommend using either simple 
local::lib or perlbrew in combination with cpanm.

https://metacpan.org/module/perlbrew
https://metacpan.org/module/cpanm

chris


On 02/07/2012 02:55 PM, Scott Cain wrote:
> hi Cassandra,
>
> I don't have an answer for you at the moment.  It seems to me that
> using local::lib is a good idea, but I've never found a good tutorial
> for using it, so I haven't.  Perhaps someone else on the list can
> suggest one.
>
> The other thing I just wanted to mention as the admin that approved
> your message--I came very close to deleting it from the queue without
> looking at it because it is not unusual for spam messages to have
> generic subjects like "help!"  (just for future reference :-)
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>  wrote:
>> Hi,
>>
>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>> installed becaused I have already write some scripts but I'm biologist so...
>> not pretty sure about what messages say.
>>
>> My perl version:
>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>> My computer:
>> Mac OS X Vesion 10.5.8
>>
>> I was following this preliminary steps:
>>
>> --------------
>>
>> PRELIMINARY PREPARATION
>>
>>     This is optional, but regardless of your subsequent choice of
>>     installation method, it will help to carry out the following steps.
>>     They will increase the likelyhood of installation success
>>     (especially of optional dependencies).
>>
>>       * Upgrade CPAN:
>>
>>   >perl -MCPAN -e shell
>>   cpan>install Bundle::CPAN
>>   cpan>q				
>>
>>       * Install/upgrade Module::Build, and make it your preferred
>>         installer:
>>
>>   >cpan
>>   cpan>install Module::Build
>>   cpan>o conf prefer_installer MB
>>   cpan>o conf commit
>>   cpan>q
>>
>>       * Install the expat library by whatever method is
>>         appropriate for your system.
>>
>>       * If your expat library is installed in a non-standard location,
>>         tell CPAN about it:
>>
>>   >cpan
>>   cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>> EXPATINCPATH=/non-standard/include"
>>   cpan>o conf commit
>>
>> --------------
>>
>> And I think I did "Upgrade CPAN properly" but when I tried the next one it
>> started asking too many things to me, and finally it stopped due to "some
>> problems". In text file you can see the whole process.
>> What did I do wrong?
>>
>>
>> After solving these preliminary steps, what should I do? What exactly .tar
>> or .whatever should I download to install?
>>
>> I don't see the difference between installing it through "built.PL" or
>>   CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>>
>> * I went to Fink webpage and what I expected to see was "hello! download
>> Bioperl simply clicking here!" but far from this, what it seems is that
>> first I have to download some kinf of Fink-program before starting with
>> Bioperl... is it something close to this?
>>
>> I'm sorry, too many questions... But I really want to learn to use Bioperl
>> but I have no people to ask it face to face.
>>
>> Thank you so much,
>>
>> Casandra
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>



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