Installing Modules

You can find thousands of Perl Modules on CPAN, the Comprehensive Perl Archive Network:

http://www.cpan.org

Installing Modules Manually

Search for the module on CPAN using the keyword search. When you find it, download the .tar.gz module. Then install it like this:

% tar zxvf bioperl-0.7.1.tar.gz
bioperl-0.7.1/
bioperl-0.7.1/Bio/
bioperl-0.7.1/Bio/DB/
bioperl-0.7.1/Bio/DB/Ace.pm
bioperl-0.7.1/Bio/DB/GDB.pm
bioperl-0.7.1/Bio/DB/GenBank.pm
bioperl-0.7.1/Bio/DB/GenPept.pm
bioperl-0.7.1/Bio/DB/NCBIHelper.pm
bioperl-0.7.1/Bio/DB/RandomAccessI.pm
bioperl-0.7.1/Bio/DB/SeqI.pm
bioperl-0.7.1/Bio/DB/SwissProt.pm
bioperl-0.7.1/Bio/DB/UpdateableSeqI.pm
bioperl-0.7.1/Bio/DB/WebDBSeqI.pm
bioperl-0.7.1/Bio/AlignIO.pm

%  perl Makefile.PL
Generated sub tests. go make show_tests to see available subtests
...
Writing Makefile for Bio

% make
cp Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm
cp Bio/Root/Err.pm blib/lib/Bio/Root/Err.pm
cp Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm
cp bioback.pod blib/lib/bioback.pod
cp Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm
cp Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm
cp Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm
cp Bio/Tools/Blast/Run/postclient.pl blib/lib/Bio/Tools/Blast/Run/postclient.pl
cp Bio/LiveSeq/Intron.pm blib/lib/Bio/LiveSeq/Intron.pm
...
Manifying blib/man3/Bio::LiveSeq::Exon.3
Manifying blib/man3/Bio::Location::CoordinatePolicyI.3
Manifying blib/man3/Bio::SeqFeature::Similarity.3

% make test
PERL_DL_NONLAZY=1 /net/bin/perl -Iblib/arch -Iblib/lib -I/net/lib/perl5/5.6.1/i686-linux -I/net/lib/perl5/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/AAChange..........ok                                                       
t/AAReverseMutate...ok                                                       
t/AlignIO...........ok                                                       
t/Allele............ok
...
t/WWW...............ok                                                       
All tests successful, 95 subtests skipped.
Files=60, Tests=1011, 35 wallclock secs (25.47 cusr +  1.60 csys = 27.07 CPU)

% make install
Installing /net/lib/perl5/site_perl/5.6.1/bioback.pod
Installing /net/lib/perl5/site_perl/5.6.1/biostart.pod
Installing /net/lib/perl5/site_perl/5.6.1/biodesign.pod
Installing /net/lib/perl5/site_perl/5.6.1/bptutorial.pl
...

If you have an older version of the tar program, you may need to replace the first step with this:

% gunzip -c bioperl-0.7.1.tar.gz | tar xvf -

Installing Modules Using the CPAN Shell

Perl has a CPAN module installer built into it. You run it like this:

% perl -MCPAN -e shell

cpan shell -- CPAN exploration and modules installation (v1.59_54)
ReadLine support enabled

cpan>

From this shell, there are commands for searching for modules, downloading them, and installing them.

[The first time you run the CPAN shell, it will ask you a lot of configuration questions. Generally, you can just hit return to accept the defaults. The only trick comes when it asks you to select CPAN mirrors to download from. Choose any ones that are in your general area on the Internet and it will work fine.]

Here is an example of searching for the Text::Wrap program and installing it:

cpan> i /Wrap/
Going to read /bush_home/bush1/lstein/.cpan/sources/authors/01mailrc.txt.gz
CPAN: Compress::Zlib loaded ok
Going to read /bush_home/bush1/lstein/.cpan/sources/modules/02packages.details.txt.gz
  Database was generated on Tue, 16 Oct 2001 22:32:59 GMT
CPAN: HTTP::Date loaded ok
Going to read /bush_home/bush1/lstein/.cpan/sources/modules/03modlist.data.gz
Distribution    B/BI/BINKLEY/CGI-PrintWrapper-0.8.tar.gz
Distribution    C/CH/CHARDIN/MailQuoteWrap0.01.tgz
Distribution    C/CJ/CJM/Text-Wrapper-1.000.tar.gz
...
Module          Text::NWrap     (G/GA/GABOR/Text-Format0.52+NWrap0.11.tar.gz)
Module          Text::Quickwrap (Contact Author Ivan  Panchenko )
Module          Text::Wrap      (M/MU/MUIR/modules/Text-Tabs+Wrap-2001.0929.tar.gz)
Module          Text::Wrap::Hyphenate (Contact Author Mark-Jason Dominus )
Module          Text::WrapProp  (J/JB/JBRIGGS/Text-WrapProp-0.03.tar.gz)
Module          Text::Wrapper   (C/CJ/CJM/Text-Wrapper-1.000.tar.gz)
Module          XML::XSLT::Wrapper (M/MU/MULL/XML-XSLT-Wrapper-0.32.tar.gz)
41 items found

cpan> install Text::Wrap
Running install for module Text::Wrap
Running make for M/MU/MUIR/modules/Text-Tabs+Wrap-2001.0929.tar.gz
CPAN: LWP::UserAgent loaded ok
Fetching with LWP:
  ftp://archive.progeny.com/CPAN/authors/id/M/MU/MUIR/modules/Text-Tabs+Wrap-2001.0929.tar.gz
CPAN: MD5 loaded ok
Fetching with LWP:
  ftp://archive.progeny.com/CPAN/authors/id/M/MU/MUIR/modules/CHECKSUMS
Checksum for /bush_home/bush1/lstein/.cpan/sources/authors/id/M/MU/MUIR/modules/Text-Tabs+Wrap-2001.0929.tar.gz ok
Scanning cache /bush_home/bush1/lstein/.cpan/build for sizes
Text-Tabs+Wrap-2001.0929/
Text-Tabs+Wrap-2001.0929/MANIFEST
Text-Tabs+Wrap-2001.0929/CHANGELOG
Text-Tabs+Wrap-2001.0929/Makefile.PL
Text-Tabs+Wrap-2001.0929/t/
Text-Tabs+Wrap-2001.0929/t/fill.t
Text-Tabs+Wrap-2001.0929/t/tabs.t
Text-Tabs+Wrap-2001.0929/t/wrap.t
Text-Tabs+Wrap-2001.0929/README
Text-Tabs+Wrap-2001.0929/lib/
Text-Tabs+Wrap-2001.0929/lib/Text/
Text-Tabs+Wrap-2001.0929/lib/Text/Wrap.pm
Text-Tabs+Wrap-2001.0929/lib/Text/Tabs.pm

  CPAN.pm: Going to build M/MU/MUIR/modules/Text-Tabs+Wrap-2001.0929.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for Text
cp lib/Text/Wrap.pm blib/lib/Text/Wrap.pm
cp lib/Text/Tabs.pm blib/lib/Text/Tabs.pm
Manifying blib/man3/Text::Wrap.3
Manifying blib/man3/Text::Tabs.3
  /usr/bin/make  -- OK
Running make test
PERL_DL_NONLAZY=1 /net/bin/perl -Iblib/arch -Iblib/lib -I/net/lib/perl5/5.6.1/i686-linux -I/net/lib/perl5/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/fill..............ok
t/tabs..............ok
t/wrap..............ok
All tests successful.
Files=3, Tests=37,  0 wallclock secs ( 0.20 cusr +  0.00 csys =  0.20 CPU)
  /usr/bin/make test -- OK
Running make install
Installing /net/lib/perl5/5.6.1/Text/Wrap.pm
Installing /net/man/man3/Text::Wrap.3
Installing /net/man/man3/Text::Tabs.3
Writing /net/lib/perl5/5.6.1/i686-linux/auto/Text/.packlist
Appending installation info to /net/lib/perl5/5.6.1/i686-linux/perllocal.pod
  /usr/bin/make install UNINST=1 -- OK

cpan> quit
Lockfile removed.

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