[Bioperl-l] help!

Dave Messina David.Messina at sbc.su.se
Tue Feb 7 17:39:48 EST 2012


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/
>
>



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