[Bioperl-l] Installation on OS X Lion

Miguel A. Amat miquel.amat at me.com
Wed Aug 24 13:48:06 EDT 2011


Thanks for all the help; I finally got it to work.  Here are the steps I took:

upgraded CPAN and used latest version of BioPerl 
installed dependencies in interactive mode, but GD failed.
Quit the installation and tried “install GD-SVG”;  this one seems to have less functionality than GD, but it worked.  
Installed Bio::Perl.  
Then, installed Bio::ASN1::EntrezGene






Best.


On Aug 24, 2011, at 10:31 AM, Scott Cain wrote:

> Hi Miguel,
> 
> Did you try the installer for snow leopard on sourceforge:
> 
>  http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/libgd-MacOSX/
> 
> I don't know if it will work on lion but I don't have a copy of lion yet to try it out on.
> 
> Scott
> 
> 
> Sent from my iPhone
> 
> On Aug 23, 2011, at 11:25 PM, Miguel A Amat <miquel.amat at me.com> wrote:
> 
>> Thanks for the feedback, Chris. Now I just need to get GD to install ...
>> 
>> On Aug 23, 2011, at 8:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> Try installing the latest version from CPAN; this bypasses the Bio::ASN1::EntrezGene req.  DBD::mysql is only needed if you intend on using modules requiring that functionality.
>>> 
>>> chris
>>> 
>>> On Aug 23, 2011, at 3:11 PM, Miguel A. Amat wrote:
>>> 
>>>> I am trying to install bioperl on mac os x 10.7 but ran into problems with the dependency packages Bio::ASN1::EntrezGene and DBD::mysql.
>>>> 
>>>> I am running the latest version of CPAN and perl -v 5.12.3 and the BioPerl-1.6.1 package.  The installation was being conducted interactively through via the "perl Build.PL" command.
>>>> 
>>>> Can you provide some help, or suggest an alternative way of installing BioPerl?
>>>> _______________________________________________
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>>> 
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