[Bioperl-l] INSTALL and INSTALL.WIN

Barry Moore barry.moore at genetics.utah.edu
Tue Oct 17 14:07:12 EDT 2006


In fact, I think it was you who taught me that trick in the first place.

B

On Oct 17, 2006, at 11:40 AM, Brian Osborne wrote:

> 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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>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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>



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