[Bioperl-l] INSTALL and INSTALL.WIN

Barry Moore barry.moore at genetics.utah.edu
Tue Oct 17 12:57:48 EDT 2006


lynx -dump http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix

does a reasonable job of textifying html.  You get the links as  
numbered references at the bottom or:

lynx -dump http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix |  
perl -ane 's/\[?\[\d+\](edit\])?//g;print'

to remove the links all together.

Barry

P.S.  Looks like this:

    #Creative Commons copyright

Installing Bioperl for Unix

 From BioPerl

    Jump to: navigation, search

Contents

      * 1 BIOPERL INSTALLATION
      * 2 SYSTEM REQUIREMENTS
      * 3 OPTIONAL
      * 4 ADDITIONAL INSTALLATION INFORMATION
      * 5 THE BIOPERL BUNDLE
      * 6 INSTALLING BIOPERL THE EASY WAY USING CPAN
      * 7 INSTALLING BIOPERL THE EASY WAY USING GNU 'make'
      * 8 WHERE ARE THE MAN PAGES?
      * 9 EXTERNAL PROGRAMS
           + 9.1 Environment Variables
      * 10 INSTALLING BIOPERL SCRIPTS
      * 11 INSTALLING BIOPERL IN A PERSONAL MODULE AREA
      * 12 INSTALLING BIOPERL MODULES THE HARD WAY
      * 13 USING MODULES NOT INSTALLED IN THE STANDARD LOCATION
      * 14 THE TEST SYSTEM
      * 15 BUILDING THE OPTIONAL bioperl-ext PACKAGE
           + 15.1 CONFIGURING for BSD and Solaris boxes
           + 15.2 INSTALLATION
         * 16 DEPENDENCIES AND Bundle::BioPerl


BIOPERL INSTALLATION

    Bioperl has been installed on many forms of Unix, Win9X/NT/2000/XP,
    and on Mac OS X (see the PLATFORMS file for more details).  
Following are
    instructions  for  installing Bioperl for Unix/Linux/Mac OS X;  
Windows
    installation instructions can be found here. For installing  
Bioperl for
    Mac OS X using Fink, see Getting BioPerl.


SYSTEM REQUIREMENTS

      * Perl 5.005 or later; version 5.6 and greater are recommended.  
Note
        that most modules will work with earlier versions of Perl.  
The only ones
        that will not are Bio::SimpleAlign and the Bio::Index::*  
modules. If
        you don't need these modules and you want to install Bioperl  
using an
        earlier version of Perl, edit the "require 5.005;" line in  
Makefile.PL
        as necessary.

      * External modules: Bioperl uses functionality provided in  
other Perl
        modules. Some of these are included in the standard perl  
package but
        some  need to be obtained from the CPAN site. The list of  
external
        modules is included at the bottom of this document.

    The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of  
these
    external modules easy. Simply install the bundle using your CPAN  
shell and
    all necessary modules will be installed. See THE BIOPERL BUNDLE,  
below.


OPTIONAL

      * ANSI  C  or  GNU  C  compiler  (gcc)  for  XS  extensions (the
        bioperl-ext package; see BUILDING THE OPTIONAL bioperl-ext
        PACKAGE, below).



ADDITIONAL INSTALLATION INFORMATION

      * Additional information on Bioperl and MAC OS:
           + OS 9 - http://bioperl.org/Core/mac-bioperl.html
           + OSX-http://www.tc.umn.edu/~cann0010/ 
Bioperl_OSX_install.html
           + OS X - Installing using Fink (in Getting BioPerl)



THE BIOPERL BUNDLE

    You typically need root privileges to install using CPAN. If you  
don't
    have these privileges please see INSTALLING BIOPERL IN A PERSONAL  
MODULE
    AREA for additional information.

    Install Bundle::Bioperl using CPAN. One way:
 >perl -MCPAN -e "install Bundle::BioPerl"

    Another way:
 >perl -MCPAN -e shell
cpan>install Bundle::BioPerl



On Oct 17, 2006, at 8:04 AM, Chris Fields wrote:

> There isn't a very easy way since so many links have to be removed/ 
> modified.
> I have found a few CPAN modules that could help, but for now I just  
> dump the
> text output from a text browser (elinks) using the 'printable  
> version' page
> and hand-edit, which works very quickly.  That works for the time  
> being
> until I can find another more automated solution.
>
> Fortunately there have been very few edits to either INSTALL wiki  
> page so
> they should remain relatively stable.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>> -----Original Message-----
>> From: Nathan S. Haigh [mailto:n.haigh at sheffield.ac.uk]
>> Sent: Tuesday, October 17, 2006 6:46 AM
>> To: Chris Fields
>> Cc: bioperl-l
>> Subject: Re: [Bioperl-l] INSTALL and INSTALL.WIN
>>
>> Chris Fields wrote:
>>> The general consensus was to keep text versions available; we could
>>> add URL links to the wiki pages for the most up-to-dat version.   
>>> BTW,
>>> I have modified INSTALL already.  INSTALL.WIN is next in line (I was
>>> waiting for your changes).
>>>
>> Is it possible to generate these files from the wiki whenever  
>> there is a
>> release? I now edits shouldn't be too severe or too often - but I can
>> see things getting a little messy/annoying if edits have to be  
>> made in 2
>> places.
>>
>> Nath
>
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> Bioperl-l at lists.open-bio.org
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