[Bioperl-l] help!

casandra mcasandrariera at gmail.com
Tue Feb 7 17:46:42 EST 2012


Thank you both,
before I received Dave's email I was answering the following:

Hello Warren,

I've repeated those steps just in case, here I show you:

maccasandra:~ mcasandrariera$ vi .bash_profile
maccasandra:~ mcasandrariera$ more .bash_profile
export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I get the same "result". Am I supposed to get something different?"

And now I tried what Dave ask me:

maccasandra:bioperl-live mcasandrariera$ printenv PERL5LIB
/Users/mcasandrariera/src/bioperl-live
maccasandra:bioperl-live mcasandrariera$

I have to say it's very nice from you to help me, specially you, Dave, who
translates all this into casandra's-super-dummie language..

Cas.

El 7 de febrero de 2012 23:39, Dave Messina <David.Messina at sbc.su.se>escribió:

> Hi Casandra,
>
> (Wayne already answered this much more succinctly than me, but here is my
> answer anyway.)
>
>
> I think you're almost there.
>
> The fact that you get no error message when you type
>  perl -e "use Bio::SeqIO;"
>
> in the directory src/bioperl-live/ tells me that probably Perl doesn't
> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
> tells Perl that it should look for Perl modules in the directories named in
> the environmental variable PERL5LIB.
>
> If you type
>
> printenv PERL5LIB
>
> do you see
>
> /Users/mcasandrariera/src/bioperl-live
>
> ?
>
> If not, then redo steps 5-10 and then try typing
> printenv PERL5LIB
>
> again. Make sure that in step 8, instead of
>
> export PERL5LIB=/Users/dave/src/bioperl-live
>
> you type
>
> export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
>
>
> To answer your other questions:
>
> although I don't know what src means...
>
>
> src is just a directory name. It's short for "source", which itself is
> really short for "source code". src the name of the directory where I keep
> all of my source code libraries like BioPerl.
>
>
> 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).
>>
>
> The short answer is that by following the zero-install instructions, you
> won't be able use some parts of BioPerl (which I'm betting you won't need
> right away).
>
> Chris and Scott's advice is correct and the right way to go in the long
> run. Once you've gotten your feet wet a bit and become more familiar with
> Perl and BioPerl, you may want to come back to their approach and try it
> again.
>
>
> Best,
> Dave
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 23:05, casandra <mcasandrariera at gmail.com> wrote:
>
>> 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/
>>
>>
>


-- 
Casandra Riera
+34 629774181
Barcelona, Spain.

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



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