[Bioperl-l] help!

Warren W. Kretzschmar wkretzsch at gmail.com
Tue Feb 7 17:30:37 EST 2012


Hi Cassandra,
Do make sure you follow steps 6-10 (below) because bioperl is not in your
include path yet.  Without adding bioperl to your include path, bioperl
will only work when you are running programs while in the bioperl-live
dir.  This is because the current dir is usually added to the perl include
list.

   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.

Warren
--
In God we trust, all others bring data. - William Edwards Deming


On Tue, Feb 7, 2012 at 10:05 PM, 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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>



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