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--- tutorials:perl_cpan [2012/03/01 13:57] – created chkuo
+++ tutorials:perl_cpan [2012/03/01 14:02] (current) – chkuo
@@ Line 4: / Line 4: @@
   * [[http://www.cpan.org/|CPAN]] is a large collection of perl modules.
-==== Installing modules ====
+===== Installing modules =====
 To call the CPAN shell interface, use:
 <code bash>
@@ Line 11: / Line 11: @@
 Using sudo allows for system-wide installation of new modules. When the call is successful, you should see a shell interface:
-<code sh>
+<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'
@@ Line 37: / Line 41: @@
 Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
 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>
-# the installer will run a bunch of tests here
-# a small number of tests are likely to fail
+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>
-# to install anyway, use 'force install'
 cpan[3]> force install CJFIELDS/BioPerl-1.6.1.tar.gz
+</code>