[Bioperl-l] problem with bioperl install

Chris Fields cjfields at illinois.edu
Mon Jun 1 13:15:42 EDT 2009

On Jun 1, 2009, at 11:27 AM, Dan Bolser wrote:

> 2009/6/1 Chris Fields <cjfields at illinois.edu>:
> ...
>> for installation.  You need to use 'sudo' to install anything / 
>> Library/Perl
>> on Mac (unless you are already 'root', but on recent OS X version  
>> logging in
> ...
> local::lib is supposed to take care of this. Is this broken on Mac?
> Building stuff as root is generally considered to be bad.

You can install to a local lib, yes, but cpan needs to be manually  
configured to do this; I don't think it is automatically configured to  
do so in OS X, eg. it defaults to /Library/Perl.

Frankly, I sidestep the whole issue with my own custom perl  
installation, but that's me.

>> I just noticed nothing is mentioned along these lines in the  
>> installation
>> docs, so we'll need to update those.
> I tried to write down a clear 'recipe' for getting things installed
> (this was actually on the GMod wiki). I really think the install docs
> could be improved. Sometimes less verbose is better.
> Dan

True, but I would much rather have reasonable instructions that  
outline most installation issues than ones that aren't detailed enough.

My thought is to strip down the INSTALL doc that comes with BioPerl  
down to the essentials and point to the wiki for the more detailed  
ones (including problems encountered).  It's too hard to maintain both  
and backport the wiki into plain text.


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