Installation using PPM is preferred since it is easier, but if you run into problems, or a PPM isn't available for the version/package of BioPerl you want, or you want to choose which optional dependencies to install, you can install manually by downloading the appropriate package or by using CPAN. In fact both methods ultimately need nmake to be installed, CPAN to be upgraded to >= v1.81, Module::Build to be installed (>= v0.2805) and Test::Harness to be upgraded to >= v2.62:
You can now follow the unix instructions for installing using CPAN, or install manually:
The advantage of this approach is it's stepwise, so it's easy to stop and analyze in case of any problem.
Download, then unpack the appropriate package. For example:
>tar xvfz BioPerl-1.6.1.tar.gz >cd BioPerl-1.6.1
Now issue the build commands:
>perl Build.PL >./Build test
If you've installed everything perfectly and all the network connections are working then you may pass all the tests run in the './Build test' phase. It's also possible that you may fail some tests. Possible explanations: problems with local Perl installation, network problems, previously undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that there are over 800 modules in Bioperl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl.
If you decide that the failed tests will not affect how you intend to use Bioperl and you'd like to install anyway, or if all tests were fine, do:
However, if you're concerned about a failed test and need assistance or advice then contact email@example.com.
To './Build install' you need write permission in the perl5/site_perl/source area (or similar, depending on your environment). Usually this will require you becoming root, so you will want to talk to your systems manager if you don't have the necessary privileges.