[Bioperl-l] Bioperl Installation

[Scott Cain]

Always, always, always reply to the list, as the original author of  
the email that you are replying to doesn't always know the answer,  
like now.  I don't recall how I installed libxslt.  In fact, I don't  
remember doing it.  Have you searched your hard drive?  I think it  
gets installed with the developers tools.

Scott

On Jul 6, 2009, at 4:01 PM, Steven McGowan wrote:

> Hi Scott,
>
> I removed my previous install with rm -rf ~/.cpan/build/*
>
> I've tried re-installing (install C/CJ/CJFIELDS/BioPerl- 
> db-1.6.0.tar.gz), and upon installing have noticed the error:
>
> Checking prerequisites...
>  - ERROR: Data::Stag is not installed
>
> so i have then quit out of the install, and entered "install  
> Data::Stag" in>CPAN
>
> but receive the following error messages:
>
> External Module XML::LibXSLT, XSLT,
>  is not installed on this computer.
>   Data::Stag::XSLTHandler in Data::Stag needs it for XSLT  
> Transformations
>
> External Module XML::Parser::PerlSAX, SAX Handler,
>  is not installed on this computer.
>   Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>
> External Module GD, Graphical Drawing Toolkit,
>  is not installed on this computer.
>   stag-drawtree.pl in Data::Stag needs it for drawing trees
>
> External Module Graph::Directed, Generic Graph data stucture and  
> algorithms,
>  is not installed on this computer.
>   Data::Stag::GraphHandler in Data::Stag needs it for transforming  
> stag trees to graphs
>
> External Module Tk, Tk,
>  is not installed on this computer.
>   stag-view.pl in Data::Stag needs it for tree viewer
>
> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's  
> lacking Data::Stag who's install is lacking the list above. How  
> would i go about installing the above list? is there an easier way  
> or something i'm doing wrong?
>
> Thanks,
>
> Stephen
>
> > From: cain.cshl at gmail.com
> > To: David.Messina at sbc.su.se
> > Subject: Re: [Bioperl-l] Bioperl Installation
> > Date: Mon, 6 Jul 2009 15:48:21 -0400
> > CC: stevey_mac2k2 at hotmail.com; Bioperl-l at lists.open-bio.org
> >
> > After you get make installed, you may need to reconfigure cpan so it
> > knows where to find it. Do this:
> >
> > sudo cpan
> >
> > (Assuming you want the libraries installed in the system paths)
> >
> > cpan> o conf init
> >
> > You can probably answer yes to the "do you want me to automatically
> > configure" question, and it should sense that make is now present.  
> If
> > not, do it again and answer "no" and accept all of the defaults  
> until
> > it gets to the part about where make is.
> >
> > Scott
> >
> > On Jul 6, 2009, at 3:38 PM, Dave Messina wrote:
> >
> >> Hi Stephen,
> >> This is on a Mac, correct?
> >>
> >> You need to install the developer tools first. The key line in your
> >> log is:
> >>
> >> Can't test without successful make
> >>
> >>
> >> Admittedly, that's cryptic. What it means is that it needs the  
> program
> >> called make. That program is installed when you install the
> >> developer tools.
> >>
> >>
> >> Go to developer.apple.com and create an account if you don't  
> already
> >> have
> >> one.
> >>
> >>
> >> Go to the Mac Dev Center, and click on "Xcode 3".
> >>
> >>
> >> This should be the right link:
> >>
> >> Xcode 3<https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20414
> >>>
> >>
> >> You'll need to login to get to it, and then you'll get to the
> >> download page
> >> for the massive 986 MB Xcode 3.1.3 download.
> >>
> >> After you run the Xcode installer, you can check in Terminal that
> >> you've got
> >> 'make' installed by typing:
> >>
> >> which make
> >>
> >> on the command line. It should give you the answer
> >> make is /usr/bin/make
> >>
> >> If it does, then you're good to try again with the bioperl install.
> >>
> >> Dave
> >> _______________________________________________
> >> 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
> >
> >
> >
> >
>
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research