[Bioperl-l] help!

casandra mcasandrariera at gmail.com
Tue Feb 7 17:05:16 EST 2012


Ok, this is what happened. I guess this mean it worked, didn't it?

Last login: Tue Feb  7 22:47:16 on ttys000
maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
Can't locate Bio/SeqIO.pm in @INC (@INC contains:
/Users/mcasaandrariera/src/bioperl-live
/Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
/Network/Library/Perl/5.12/darwin-thread-multi-2level
/Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
/System/Library/Perl/5.12/darwin-thread-multi-2level
/System/Library/Perl/5.12
/System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.12 .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I took your src name (I hadn't any better suggestion, although I don't know
what src means... :P)

Thank you so much to all of you! I have to say that it was a big relief
reading Dave telling so simple things :D thanks!

Maybe it will be useless to explain it to me, but, why this method isn't
"installing" Bioperl? Why I didn't need to do all those preliminary steps,
use Fink, and so on? I mean, if I can finally do the same (using Bioperl).

And related to the previous method I tried, I read that you were discussing
"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. " I really didn't "wanted" to use it, I chose it because it
was the default option, and, since I didn't know about the alternatives, I
thought that the default would be ok... But if what Dave said works, better
for me, I didn't really know what I was doing with thosesteps (but I want
to learn it soon! ;) )

Thank you all for your time ;)

Casandra

El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se>escribió:

> I will take the opportunity to shamelessly pimp my no-install install
> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
> Casandra is just looking to get started with BioPerl, messing with external
> libs and configs is probably overkill.
>
> Best,
> Dave
>
>
>
>  There’s a quickie, “zero-install” way to get BioPerl on your system.
>
>     1) Okay, click here to download bioperl as a zip file:
>
>     https://github.com/bioperl/bioperl-live/zipball/master
>
>
>     when it's done downloading, unzip it if your computer hasn’t done it
> automatically. On the
>     command line, you would do:
>
>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
>     or whatever the file is called. You should then have a folder with
> some ugly name like
>
>     bioperl-bioperl-live-558467a
>
>     3) rename that to
>
>     bioperl-live
>
>     4) move that folder to wherever you want to keep it. I keep mine in a
> directory called src in my
>         home directory.
>
>     So on my computer if I go to the command line and cd to that folder
> and type pwd I get:
>
>     /Users/dave/src/bioperl-live
>
>     5) in the terminal, cd to your home directory.
>
>     6) see if you have a file named .bash_profile by typing
>
>     ls -l ~/.bash_profile
>
>     7) if so, open that file in your favorite editor. if the file doesn't
> exist, just create the file.
>
>     8) put this line in your .bash_profile
>
>              export PERL5LIB=/Users/dave/src/bioperl-live
>
>     (obviously replacing my path info with wherever you chose to put
> bioperl)
>
>     9) save and close your .bash_profile
>
>   10) open a new terminal window so that the change will take effect.
>
>   11) on the command line of the new terminal, type
>
>                perl -e "use Bio::SeqIO;"
>
>     If that works, then you have "installed" bioperl. Yay!
>
>
>
>
>
>
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> 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
>> >>
>> >>
>> >>
>> >>
>> >
>> > _______________________________________________
>> > 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


-- 
Casandra Riera
+34 629774181
Barcelona, Spain.

mcasandrariera at gmail.com
http://terrainsalo.blogspot.com/



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