[Bioperl-l] INSTALL and INSTALL.WIN
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.
On Oct 17, 2006, at 11:40 AM, Brian Osborne wrote:
> 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>
>> 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.
>> P.S. Looks like this:
>> #Creative Commons copyright
>> Installing Bioperl for Unix
>> From BioPerl
>> Jump to: navigation, search
>> * 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/
>> and on Mac OS X (see the PLATFORMS file for more details).
>> Following are
>> instructions for installing Bioperl for Unix/Linux/Mac OS X;
>> 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.
>> 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
>> 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
>> modules is included at the bottom of this document.
>> The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of
>> external modules easy. Simply install the bundle using your CPAN
>> shell and
>> all necessary modules will be installed. See THE BIOPERL BUNDLE,
>> * ANSI C or GNU C compiler (gcc) for XS extensions
>> 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/
>> + OS X - Installing using Fink (in Getting BioPerl)
>> THE BIOPERL BUNDLE
>> You typically need root privileges to install using CPAN. If you
>> have these privileges please see INSTALLING BIOPERL IN A PERSONAL
>> 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/
>>> 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
>>> 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
>>>>> add URL links to the wiki pages for the most up-to-dat version.
>>>>> 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
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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