[Bioperl-l] INSTALL and INSTALL.WIN

Tue Oct 17 17:40:54 UTC 2006

Barry,

I second that. lynx does the best job of converting HTML to text I've seen.

Brian O.

On 10/17/06 12:57 PM, "Barry Moore" <barry.moore at genetics.utah.edu> wrote:

> 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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