[Bioperl-l] Re: Installing BioPerl under Mac OS X

Koen van der Drift kvddrift at earthlink.net
Thu Oct 21 06:07:46 EDT 2004

On Oct 21, 2004, at 1:27 AM, Madeleine Lemieux wrote:

> Koen,
>>> I have also installed (following each package's installation 
>>> instructions) wwwBlast (latest OS X version from NCBI), t-coffee 
>>> (the Unix version, not the Mac one), clustalw (the OS X version) and 
>> Just as a note, all three, as well as pTk (804.026) are also availble 
>> through fink.
> My fink (0.7.1) does not list clustalw, pTk, t-coffee or wwwBlast 
> among its packages so I just downloaded the source or executables that 
> were available. I've used fink several times but don't know much about 
> it. Is there some way other than using the list option to find out 
> what packages are available?

They are called:


You may have to enable the unstable tree in fink to be able to install 
these, see 

> I was quite pleased to see bioperl as one of the fink packages but see 
> below for what happens when I try use fink to install bioperl-pm581. 
> Is there a log file somewhere that might contain more useful 
> information?

> ### execution of make failed, exit code 2
> Failed: compiling uri-pm581-1.30-11 failed
> LeMeiLin:~ $

That's a problem with the uri-pm581 package. Version 1.33 is now 
available, so you might want to update the fink info files (see the FAQ 
entry above).

Bioperl is part of the bindist in 0.7.1, so you can also do:

sudo apt-get install bioperl-pm581 to install it directly without 

good luck,

- Koen.

More information about the Bioperl-l mailing list