3 The following are instructions for installing BioPerl on
4 Unix, Linux, and Mac OS X. Windows installation instructions can be
10 * `Perl 5.6.1 or higher` Version 5.8 or higher is highly
11 recommended. Modules are tested against version 5.8 and
13 * `make` For Mac OS X, this requires installing the Xcode Developer
17 PRELIMINARY PREPARATION
19 These are optional, but regardless of your subsequent choice of
20 installation method, it will help to carry out the following steps.
21 They will increase the likelihood of installation success
22 (especially of the optional dependencies).
28 * Install or upgrade `Module::Build`, and make it your preferred installer:
30 cpan>install Module::Build
31 cpan>o conf prefer_installer MB
34 * Install the *expat* library by whatever method is appropriate for your system (e.g. `apt`, `yum`, `homebrew`).
37 INSTALLING BIOPERL THE EASY WAY USING CPAN
39 You can use the CPAN shell to install BioPerl. For example:
43 Or you might have the `cpan` alias installed:
47 Then find the name of the latest BioPerl package:
53 Distribution CJFIELDS/BioPerl-1.6.901.tar.gz
54 Distribution CJFIELDS/BioPerl-1.6.922.tar.gz
55 Distribution CJFIELDS/BioPerl-1.6.924.tar.gz
57 And install the most recent:
59 cpan>install CJFIELDS/BioPerl-1.6.924.tar.gz
61 If you've installed everything perfectly and all the network
62 connections are working then you will pass all the tests run in the
63 `./Build test` phase. Sometimes you may see a failed test. Remember that
64 there are over 900 modules in BioPerl and the test suite is running more
65 than 12000 individual tests, a failed test may not affect your usage
68 If there's a failed test and you think that the failed test will not
69 affect how you intend to use BioPerl then do:
71 cpan>force install C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
73 If you're concerned about a failed test and need assistance or advice
74 then contact bioperl-l@bioperl.org, and provide us the detailed
75 results of the failed install.
78 INSTALLING BIOPERL FROM GITHUB
80 The very latest version of Bioperl is at github.com. If you want this
81 version then download it from https://github.com/bioperl/bioperl-live
82 as a *zip file, or retrieve it using the command line:
84 git clone https://github.com/bioperl/bioperl-live.git
87 If you've downloaded the *zip file then unzip that and cd to the
90 Issue the build commands:
94 You will be asked a few questions about installing BioPerl scripts
95 and running various test suites, hit *return* to accept the defaults.
105 You may need root permissions in order to run `./Build install`, so you
106 will want to talk to your systems manager if you don't have the necessary
107 privileges. Or you can install the package in your own home
108 directory, see INSTALLING BIOPERL USING local::lib.
111 INSTALLING BIOPERL USING local::lib
113 If you lack permission to install Perl modules into the standard
114 system directories you can install them in your home directory
115 using `local::lib`. The instructions for first installing
116 `local::lib` are found here:
118 https://metacpan.org/pod/local::lib
120 Once `local::lib` is installed you can install BioPerl using a
123 perl -MCPAN -Mlocal::lib -e 'CPAN::install(C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz)'
125 INSTALLING BIOPERL SCRIPTS
127 BioPerl comes with a set of production-quality scripts that are
128 kept in the scripts/ directory. You can install these scripts if you'd
129 like, simply answer the questions during `perl Build.PL`.
130 The installation directory can be specified by:
133 ./Build install --install_path script=/foo/scripts
135 By default they install to */usr/bin* or similar, depending on platform.
140 The BioPerl test system is located in the *t/* directory and is
141 automatically run whenever you execute the `./Build test` command.
143 The tests have been organized into groups
144 based upon the specific task or class the module being tested belongs
145 to. If you want to investigate the behavior of a specific test such as
146 the Seq test you would type:
148 ./Build test --test_files t/Seq/Seq.t --verbose
150 The `--test_files` argument can be used multiple times to try a set of test
151 scripts in one go. The `--verbose` arguement outputs the detailed test results, instead of just the summary you see during `./Build test`.
153 The `--test-files` argument can also work as a glob. For instance, to
154 run tests on all SearchIO modules, use the following:
156 ./Build test --test_files t/SearchIO* --verbose
158 If you are trying to learn how to use a module, often the test suite
159 is a good place to look. All good extreme programmers try and write a
160 test BEFORE they write the module to insure that their module behaves
161 the way they expect. You'll notice some `ok` and `skip` commands in a
162 test, this is part of the Perl test suite that signifies a passed test
163 with an 'ok N', where N is the test number. Alternatively you can tell
164 Perl to skip tests. This is useful when, for example, your test
165 detects that the network is not present and thus should skip, not
166 fail, any tests that require a network connection.
168 The core developers have indicated that future releases of BioPerl
169 will require that new modules come with a test suite with some minimal
170 tests. Modules that lack adequate tests or could otherwise be
171 considered 'unstable' will be moved into a separate developer
172 distribution until adequate tests are added and the API stablizes.