[Bioperl-l] help!

Scott Cain scott at scottcain.net
Tue Feb 7 16:12:19 EST 2012


Yes, but those doc don't address exactly the problem Cassandra is
having, that she wants to use local::lib, but there need to be some
prereqs installed, but they can't be because she chose to use
local::lib, and it's not installed.  That's all fine if you're not a
newbie and know how to properly install the prereqs before using the
cpan shell, but when following instructions that say "use local::lib",
I find that the instructions are completely insufficient in actually
getting the desired software installed.  Thus the need for a good
tutorial.

Scott


On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 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
>>
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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