[Bioperl-l] help!

Dave Messina David.Messina at sbc.su.se
Tue Feb 7 18:33:34 EST 2012


Ah right, that's a good point. Well, don't I feel like the asshole. :)

Once local::lib and cpanm are installed, it's possible to run cpanm on the
tarball downloaded from github, right?

i.e.
cpanm bioperl-live-bioperl-release-**1-5-1-rc4-4318-g342e587.zip

And that should take care of dependencies, then, correct?


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).


Agreed, that's a great idea.


Best,
Dave




On Tue, Feb 7, 2012 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> 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 <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 <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<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<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<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/perlbrew>
>>             > https://metacpan.org/module/**cpanm<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<Bioperl-l at lists.open-bio.org>
>> >
>>
>>             >>> http://lists.open-bio.org/**mailman/listinfo/bioperl-l<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<Bioperl-l at lists.open-bio.org>
>> >
>>
>>             > http://lists.open-bio.org/**mailman/listinfo/bioperl-l<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<Bioperl-l at lists.open-bio.org>
>> >
>>
>>            http://lists.open-bio.org/**mailman/listinfo/bioperl-l<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<mcasandrariera at gmail.com>
>> >
>>    http://terrainsalo.blogspot.**com/ <http://terrainsalo.blogspot.com/>
>>
>>
>>
>



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