[Bioperl-l] help!
Chris Fields
cjfields at illinois.edu
Tue Feb 7 22:50:29 UTC 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
>
> _______________________________________________
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>
>
>
>
>
> --
> 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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