[Bioperl-l] help!

Chris Fields cjfields at illinois.edu
Tue Feb 7 16:27:38 EST 2012


Right, I see.  However, Casandra didn't mention using local::lib, just 
using CPAN in general (hence my initial question).

IIRC local::lib, if set up correctly, should take care of the 
installation paths for CPAN/cpanm/etc regardless whether it's bioperl or 
any other perl module.

Last I checked this didn't seem to be an issue with bioperl; I installed 
Bioperl, as well as any prereqs, Bio::DB::Sam/BigWig, Moose, 
DBD::SQLite, etc, on our local SGI using local::lib in a common project 
space (with perl 5.10.1) w/o a problem.  If there is a problem specific 
to BioPerl, we should probably try to fix it and clarify any workarounds 
in the meantime.

chris

On 02/07/2012 03:12 PM, Scott Cain wrote:
> 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
>>>
>>>
>>>
>>>
>>
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