[Bioperl-l] help!
Dave Messina
David.Messina at sbc.su.se
Tue Feb 7 23:33:34 UTC 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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