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BioPerl-1.007002
/ INSTALL.md

BioPerl Installation

There are two principle ways to get BioPerl onto your system. One (and the still most common) is to install it locally on your machine. To do this, refer to and follow the instructions below for installing BioPerl on Unix, Linux, and Mac OS X. For installing BioPerl on Windows, please read INSTALL.WIN. The other way is to use a Docker image with a BioPerl build, whether one we support or one you build yourself.

Installing BioPerl locally

Note that this documentation is for Unix, Linux, and MacOSX. For installing BioPerl on Windows, please read INSTALL.WIN.

System Requirments

Preliminary Preparation

These are optional, but regardless of your subsequent choice of installation method, it will help to carry out the following steps. They will increase the likelihood of installation success (especially of the optional dependencies).

perl -MCPAN -e shell

cpan>install Module::Build
cpan>o conf prefer_installer MB
cpan>o conf commit

Installing BioPerl the Easy Way

We highly recommend using cpanminus for installing BioPerl and its dependencies. We also highly recommend (if possible) using a tool like perlbrew to locally install a modern version of perl (a version that is higher than perl 5.16). The linked pages describe how to install each tool; make sure if you install perlbrew that you follow up with installing cpanm:

perlbrew install-cpanm

Then, you can install BioPerl:

cpanm Bio::Perl

You can also use the older CPAN shell to install BioPerl. For example:

perl -MCPAN -e shell

Or you might have the cpan alias installed:

cpan

Then find the name of the latest BioPerl package:

cpan>d /bioperl/
 ....

 Distribution    C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
 Distribution    C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
 Distribution    C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

And install the most recent:

cpan>install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

If you've installed everything perfectly and all the network connections are working then you will pass all the tests run in the ./Build test phase. Sometimes you may see a failed test. Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a failed test may not affect your usage of BioPerl.

If there's a failed test and you think that the failed test will not affect how you intend to use BioPerl then do:

cpan>force install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

If you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org, and provide us the detailed results of the failed install.

Installing BioPerl from Github

NOTE: We generally do not recommend installing the latest code from Github unless you absolutely need the latest bug fixes.

The very latest version of Bioperl is at github.com. If you want this version then download it from https://github.com/bioperl/bioperl-live as a tar.gz or zip file, or retrieve it using the command line:

git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live

Using cpanm

If you have cpanm, you can install within the checkout directory by simply using:

cpanm --interactive .

to run interative installation, or you can leave out the --interactive flag to accept the defaults.

Using the Installation Script

Issue the build commands:

perl Build.PL

You will be asked a few questions about installing BioPerl scripts and running various test suites, hit return to accept the defaults.

Test:

./Build test

Install:

./Build install

You may need root permissions in order to run ./Build install, so you will want to talk to your systems manager if you don't have the necessary privileges. Or you can install the package in your own home directory, see INSTALLING BIOPERL USING local::lib.

Installing Bioperl using local::lib

If you lack permission to install Perl modules into the standard system directories you can install them in your home directory using local::lib. The instructions for first installing local::lib are found in the link.

Once local::lib is installed you can install BioPerl using a command like this:

perl -MCPAN -Mlocal::lib -e 'CPAN::install(C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz)'

Installing BioPerl Scripts

BioPerl comes with a set of production-quality scripts that are kept in the scripts/ directory. You can install these scripts if you'd like, simply answer the questions during perl Build.PL. The installation directory can be specified by:

perl Build.PL ./Build install --install_path script=/foo/scripts

By default they install to /usr/bin or similar, depending on platform.

The Test System

The BioPerl test system is located in the t/ directory and is automatically run whenever you execute the ./Build test command.

The tests have been organized into groups based upon the specific task or class the module being tested belongs to. If you want to investigate the behavior of a specific test such as the Seq test you would type:

./Build test --test_files t/Seq/Seq.t --verbose

The --test_files argument can be used multiple times to try a set of test scripts in one go. The --verbose arguement outputs the detailed test results, instead of just the summary you see during ./Build test.

The --test-files argument can also work as a glob. For instance, to run tests on all SearchIO modules, use the following:

./Build test --test_files t/SearchIO* --verbose

You can also use the command-line tool prove to run tests as well, which is quite useful if you are developing code:

prove -lrv t/SearchIO*

If you are trying to learn how to use a module, often the test suite is a good place to look. All good extreme programmers try and write a test BEFORE they write the module to insure that their module behaves the way they expect. You'll notice some ok and skip commands in a test, this is part of the Perl test suite that signifies a passed test with an 'ok N', where N is the test number. Alternatively you can tell Perl to skip tests. This is useful when, for example, your test detects that the network is not present and thus should skip, not fail, any tests that require a network connection.

The core developers have indicated that future releases of BioPerl will require that new modules come with a test suite with some minimal tests. Modules that lack adequate tests or could otherwise be considered 'unstable' will be moved into a separate developer distribution until adequate tests are added and the API stablizes.

Using BioPerl via Docker

If you don't have Docker installed already, instructions for how to install Docker on Linux, MacOSX, and Windows are available online.

We officially support several builds (latest, stable, and releases) hosted in the bioperl/bioperl repo on Docker Hub. These images do not have a pre-defined entrypoint. If you have a BioPerl script in the current directory, you can run it as simple as this:

docker run -t --rm -v `pwd`:/work -w /work bioperl/bioperl perl my-script.pl

Or run an interactive shell:

docker run -ti --rm -v `pwd`:/work -w /work bioperl/bioperl bash

You can also build your own Docker image of BioPerl, using the same base image and pre-built dependencies that we use. Simply build off of the bioperl/bioperl-deps image.