[Bioperl-l] Newbie question installing on MacOSX

Roy Chaudhuri roy.chaudhuri at gmail.com
Thu Jul 29 11:36:11 EDT 2010


Please copy replies to the mailing list, that way others can respond.

Try the command:
perl -MBio::Seq -e ''

If Bioperl is not installed you will get an error message starting 
"Can't locate Bio/Seq in @INC". If the command just exits silently then 
BioPerl is installed correctly.

Roy.

On 29/07/2010 16:29, James Platt wrote:
> Hi,
>
> I tried that, sorry I wasn't clear in the first post.
>
> James$ fink install bioperl-pm588
> Information about 2521 packages read in 0 seconds.
> Failed: no package found for specification 'bioperl-pm588'!
>
> I think I may have installed it through fink commander. how do i check
> in unix that it is in fact installed?
>
> Thanks,
>
> James
>
> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote:
>
>> Hi James,
>>
>> I don't know anything about Macs, but looking here:
>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink
>>
>> shouldn't the command be "fink install bioperl-pm588"?
>>
>> Roy.
>>
>> On 29/07/2010 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>



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