[Bioperl-l] help!

Chris Fields cjfields at illinois.edu
Tue Feb 7 17:50:29 EST 2012


The catch with a PERL5LIB approach for a new installation is the very
possibility that non-core dependencies will not be installed.  We'll 
have a response down the road for 'why did Bio::Foo fail with the 
following error', with an obvious missing dependency being the problem.

We've been discussing this on IRC (scott, leont and I). I tend to think 
the best solution for new users is to set them up with both local::lib 
and cpanm initially, either by simply documenting this or by getting a 
script up and running for them.  This will resolve down-stream problems 
(for instance, if the distribution is split up).

chris


On 02/07/2012 04:39 PM, Dave Messina wrote:
> 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
> <mailto: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
>     <mailto: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
>         <mailto: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 <mailto: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 <mailto: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
>             <mailto: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
>             <mailto: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
>             <tel:216-392-3087>
>             Ontario Institute for Cancer Research
>
>             _______________________________________________
>             Bioperl-l mailing list
>             Bioperl-l at lists.open-bio.org
>             <mailto:Bioperl-l at lists.open-bio.org>
>             http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>
>     --
>     Casandra Riera
>     +34 629774181 <tel:%2B34%20629774181>
>     Barcelona, Spain.
>
>     mcasandrariera at gmail.com <mailto:mcasandrariera at gmail.com>
>     http://terrainsalo.blogspot.com/
>
>



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