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How To Install BioPerl on Mac OS X Snow Leopard |
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BioPerl is a collection of Perl modules that facilitate the
development of Perl scripts for bioinformatics applications.
The easiest way to install it on Mac OS X was to use
fink,
because BioPerl requires many other perl modules preinstalled
and fink automatically installs them. Until Mac OS X 10.5
Leopard, fink binary package and BioPerl binary package for fink
were available and it was pretty easy to install BioPerl.
However, fink binary package is not available for Mac OS X 10.6
Snow Leopard as of today and it is not easy to install BioPerl
on Snow Leopard. |
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This page describes how to install fink and
BioPerl on Mac OS X 10.6 Snow Leopard. Both of them are
built from the source codes. |
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The procedure below was confirmed to work
fine on Mac OS X 10.6.4 Snow Leopard. |
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If you want to install BioPerl on Mac OS X 10.5
or earlier, you don't have to follow the procedure below.
Just install fink and BioPerl binaries.
Instruction is found here. |
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If you have any questions or comments, please
post it on our
Facebook page. |
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Up-to-date as of 10/23/2010 |
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| 1. Preparation |
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| 2. Install fink
Original installation instruction is
here |
2.1. Download
fink-0.29.14.tar.gz from
http://www.finkproject.org/download/srcdist.php
2.2. Open Applications/Utilities/Terminal and
enter commands below.
2.3. tar xfz
fink-0.29.14.tar.gz
2.4. cd fink-0.29.14
2.5. ./bootstrap
It will ask many questions. Accept
default values.
2.6. /sw/bin/pathsetup.sh
It will setup environment for fink.
2.7. fink
selfupdate-rsync
2.8. fink index -f |
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3. Install BioPerl |
3.1. fink configure
Accept default values except 'The "unstable" tree does not appear to be activated
in your fink now. Do you want to activate it? [y/N] ' Answer y for this.
3.2. fink selfupdate.
Accept default values.
3.3. fink selfupdate-rsync
3.4. fink
index -f
3.5. fink scanpackages
3.6. fink list
Find Package Name. The most recent
one for Snow Leopard is bioperl-pm5100
3.7. fink install bioperl-pm5100
Accept default values. This will
install BioPerl and required perl
modules from source codes. |
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