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====== Using the Comprehensive Perl Archive Network (CPAN) ======

===== CPAN =====
  * [[http://www.cpan.org/|CPAN]] is a large collection of perl modules.

===== Installing modules =====
To call the CPAN shell interface, use: 
<code bash>
$ sudo perl -MCPAN -e shell
</code>
Using sudo allows for system-wide installation of new modules. When the call is successful, you should see a shell interface:

<code>
cpan[1]> 
</code>

For example, if we want to install bioperl, first we can do a listing with the following command:
<code>
cpan[1]> d /bioperl/
</code>

This should generate some output similar to the following:
<code>
CPAN: Storable loaded ok (v2.20)
Going to read '/home/chkuo/.cpan/Metadata'
  Database was generated on Thu, 08 Jul 2010 06:27:10 GMT
Distribution    BIRNEY/bioperl-1.2.2.tar.gz
Distribution    BIRNEY/bioperl-1.2.3.tar.gz
Distribution    BIRNEY/bioperl-1.2.tar.gz
Distribution    BIRNEY/bioperl-1.4.tar.gz
Distribution    BIRNEY/bioperl-db-0.1.tar.gz
Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
Distribution    BIRNEY/bioperl-run-1.4.tar.gz
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CJFIELDS/BioPerl-1.6.0.tar.gz
Distribution    CJFIELDS/BioPerl-1.6.1.tar.gz
Distribution    CJFIELDS/BioPerl-db-1.6.0.tar.gz
Distribution    CJFIELDS/BioPerl-network-1.6.0.tar.gz
Distribution    CJFIELDS/BioPerl-run-1.6.1.tar.gz
Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
15 items found
</code>

From this list, we can see that the ''CJFIELDS/BioPerl-1.6.1.tar.gz'' module is what we want (the newest version). To install:
<code>
cpan[2]> install CJFIELDS/BioPerl-1.6.1.tar.gz
</code>

Usually this should work for most modules and all required dependencies should be installed automatically. Bioperl is unusual because it contains a large number of components and some tests may fail during the installation process. Often these failures do not really matter and we can proceed with force install: 
<code>
cpan[3]> force install CJFIELDS/BioPerl-1.6.1.tar.gz
</code>