[Bioperl-l] INSTALL and INSTALL.WIN
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.
P.S. Looks like this:
#Creative Commons copyright
Installing Bioperl for Unix
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 has been installed on many forms of Unix, Win9X/NT/2000/XP,
and on Mac OS X (see the PLATFORMS file for more details).
instructions for installing Bioperl for Unix/Linux/Mac OS X;
installation instructions can be found here. For installing
Mac OS X using Fink, see Getting BioPerl.
* 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::*
you don't need these modules and you want to install Bioperl
earlier version of Perl, edit the "require 5.005;" line in
* External modules: Bioperl uses functionality provided in
modules. Some of these are included in the standard perl
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
all necessary modules will be installed. See THE BIOPERL BUNDLE,
* ANSI C or GNU C compiler (gcc) for XS extensions (the
bioperl-ext package; see BUILDING THE OPTIONAL bioperl-ext
ADDITIONAL INSTALLATION INFORMATION
* Additional information on Bioperl and MAC OS:
+ OS 9 - http://bioperl.org/Core/mac-bioperl.html
+ 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"
>perl -MCPAN -e shell
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 could
>>> 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
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