[Bioperl-l] Installing bioperl-ext on Mac

Steve Chervitz sac at bioperl.org
Mon Nov 26 22:27:09 EST 2007

Hi Jon,

I'd recommend downloading it into a separate location of your choosing
(~/lib/bioperl-ext for example) and running the installer as specified
in the docs that come with the download. Then you can include the
location you installed it into via a "use lib '~/lib/bioperl-ext'"
statement at the top of your script. It may be handy to install it as
a non-root user so that you don't alter the main perl installation.

This way your ext install will stay separate from your main bioperl
and perl installations.

There are some docs about the ext packages you might want to check out
at http://www.bioperl.org/wiki/Ext_package.


On Nov 21, 2007 4:35 PM, Jonathan Binkley <binkley at genome.stanford.edu> wrote:
> Hi,
> I installed bioperl on a Mac (OS 10.4, Intel) via fink,
> which put it here:
> /sw/lib/perl5/5.8.6/Bio/
> It seems to work fine, but I need bioperl-ext for
> Smith-Waterman alignments.
> So, into which directory should I download bioperl-ext and
> run the Makefile?
> Thanks.
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> Bioperl-l at lists.open-bio.org
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