[Bioperl-l] Newbie question installing on MacOSX

Adam Witney awitney at sgul.ac.uk
Thu Jul 29 11:06:01 EDT 2010


Hi James,

You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both.

I would personally recommend installing it from source or better still install from cpan. Take a look here:

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

If you really want to use fink then take a look here:

http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink

It looks like the command for this is:

fink install bioperl-pm588

but I don't use fink any more so I am not certain of how that works.

adam


On 29 Jul 2010, at 15:18, James wrote:

> Sorry for the newbie question.
> 
> I am having trouble installing Bioperl.
> 
> I'm on MacOSX 10.5.8.
> 
> I downloaded and installed fink:
> 
> $ fink --version
> Package manager version: 0.27.13
> Distribution version: 0.9.0 i386
> 
> I then downloaded Bioperl-1.6.1, I'm trying to install it from source,
> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have
> Xcode installed etc.
> 
> '# fink install bioperl-pmXXX'
> 
> I try this:
> 
> BioPerl-1.6.1 James$ fink install BioPerl-pm
> 
> Information about 2521 packages read in 1 seconds.
> Failed: no package found for specification 'BioPerl-pm'!
> 
> 
> The version of perl I'm running is 5.8.8, I have tried 'fink install
> BioPerl588' but this doesn't work either.
> 
> Thanks very much,
> 
> James
> 
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




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