Installing BioPerl for Unix * 1 BIOPERL INSTALLATION * 2 SYSTEM REQUIREMENTS * 3 OPTIONAL * 4 ADDITIONAL INSTALLATION INFORMATION * 5 PRELIMINARY PREPARATION * 6 INSTALLING BIOPERL THE EASY WAY USING Build.PL * 7 INSTALLING BIOPERL THE EASY WAY USING CPAN * 8 WHERE ARE THE MAN PAGES? * 9 EXTERNAL PROGRAMS * 9.1 Environment Variables * 10 INSTALLING BIOPERL SCRIPTS * 11 INSTALLING BIOPERL IN A PERSONAL MODULE AREA * 12 INSTALLING BIOPERL MODULES THE HARD WAY * 13 USING MODULES NOT INSTALLED IN THE STANDARD LOCATION * 14 THE TEST SYSTEM * 15 BUILDING THE OPTIONAL bioperl-ext PACKAGE * 16.1 CONFIGURING for BSD and Solaris boxes * 16.2 INSTALLATION BIOPERL INSTALLATION For the most up-to-date installation instructions please see the BioPerl wiki: http://www.bioperl.org/wiki/Installing_BioPerl BioPerl has been installed on many forms of Unix, Win9X/NT/2000/XP, and on Mac OS X. The following are instructions for installing BioPerl for Unix/Linux/Mac OS X. Windows installation instructions can be found in INSTALL.WIN. For installing BioPerl for Mac OS X using Fink, see: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink SYSTEM REQUIREMENTS * Perl 5.6.1 or later; version 5.8 and greater are highly recommended. Modules are generally tested against perl 5.8 and above. * External modules: BioPerl uses functionality provided in other Perl modules. Some of these are included in the standard perl package but some need to be obtained from the CPAN site. The list of external modules is included in the DEPENDENCIES file. OPTIONAL * ANSI C or GNU C compiler (gcc) for XS extensions (the bioperl-ext package; see BUILDING THE OPTIONAL bioperl-ext PACKAGE, below). ADDITIONAL INSTALLATION INFORMATION * Additional information on BioPerl and MAC OS: * OS 9 - http://bioperl.org/Core/mac-bioperl.html NOTE: These are severely out-of-date and require MacPerl (the latest version of which is 5.6.1rc1). As such, we do not currently support BioPerl on OS 9 * OS X - Installing using Fink (in Getting BioPerl) PRELIMINARY PREPARATION This is optional, but regardless of your subsequent choice of installation method, it will help to carry out the following steps. They will increase the likelyhood of installation success (especially of optional dependencies). * Upgrade CPAN: >perl -MCPAN -e shell cpan>install Bundle::CPAN cpan>q * Install/upgrade Module::Build, and make it your preferred installer: >cpan cpan>install Module::Build cpan>o conf prefer_installer MB cpan>o conf commit cpan>q * Install the expat library by whatever method is appropriate for your system. * If your expat library is installed in a non-standard location, tell CPAN about it: >cpan cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include" cpan>o conf commit INSTALLING BIOPERL THE EASY WAY USING Build.PL 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 tar file. For example: >tar xvfz BioPerl-1.6.923.tar.gz >cd BioPerl-1.6.923 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 900 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: >./Build install If you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org. (You could provide us the detailed results of the failed test(s): see the `THE TEST SYSTEM' below for information on how to generate such results.) 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. It is also straightforward to install the package outside of the this standard Perl5 location. See INSTALLING BIOPERL IN A PERSONAL MODULE AREA, below. INSTALLING BIOPERL THE EASY WAY USING CPAN You can use the 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 BioPerl version you want: cpan>d /bioperl/ .... Distribution CJFIELDS/BioPerl-1.6.901.tar.gz Distribution CJFIELDS/BioPerl-1.6.922.tar.gz Distribution CJFIELDS/BioPerl-1.6.923.tar.gz Now install: cpan>install CJFIELDS/BioPerl-1.6.923.tar.gz 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 used for sequence retrieval at public database, and so on. Remember that there are over 900 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 do: cpan>force install C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz If you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org. (You could provide us the detailed results of the failed test(s): see the `THE TEST SYSTEM' below for information on how to generate such results.) WHERE ARE THE MAN PAGES? Previously, when using Makefile.PL (no longer covered in this documentation), we had to disable the automatic creation of man pages because this step was triggering a "line too long" error on some OSs due to shell constraints. If you want man pages installed use the Build.PL installation process discussed above. EXTERNAL PROGRAMS BioPerl can interface with some external programs for executing analyses. These include clustalw and t_coffee for Multiple Sequence Alignment (Bio::Tools::Run::Alignment::Clustalw and Bio::Tools::Run::Alignment::TCoffee) and blastall, blastpgp, and bl2seq for BLAST analyses (Bio::Tools::Run::StandAloneBlast), and to all the programs in the EMBOSS suite (Bio::Factory::EMBOSS). Most of the modules which 'wrap' these programs are located in the separate bioperl-run distribution; however, two commonly-used modules are still distributed with the BioPerl core (Bio::Tools::Run::StandAloneBlast, Bio::Tools::Run::RemoteBlast). Environment Variables Some modules which run external programs need certain environment variables set. If you do not have a local copy of the specific executable you do not need to set these variables. Additionally the modules will attempt to locate the specific applications in your runtime PATH variable. You may also need to set an environment variable to tell BioPerl about your network configuration if your site uses a firewall. Setting environment variables on unix means adding lines like the following to your shell *rc file. For bash or sh: export BLASTDIR=/data1/blast For csh or tcsh: setenv BLASTDIR /data1/blast Some environment variables include: +------------------------------------------------------------------------+ | Env. Variable | Description | |---------------+--------------------------------------------------------| | |Specifies where the NCBI blastall, blastpgp, bl2seq, | |BLASTDIR |etc.. are located. A 'data' directory could also be | | |present in this directory as well, you could put your | | |blastable databases here. | |---------------+--------------------------------------------------------| | |If one does not want to locate the data dir within the | |BLASTDATADIR or|same dir as where the BLASTDIR variable points, a | |BLASTDB |BLASTDATADIR or BLASTDB variable can be set to point to | | |a dir where BLAST database indexes are located. | |---------------+--------------------------------------------------------| |BLASTMAT |The directory containing the substitution matrices such | | |as BLOSUM62. | |---------------+--------------------------------------------------------| |CLUSTALDIR |The directory where the clustalw executable is located. | |---------------+--------------------------------------------------------| |TCOFFEEDIR |The directory where the t_coffee executable is located. | |---------------+--------------------------------------------------------| | |If you access the internet via a proxy server then you | | |can tell the BioPerl modules which require network | | |access about this by using the http_proxy environment | |http_proxy |variable. The value set includes the proxy address and | | |the port, with optional username/password for | | |authentication purposes | | |(e.g. http://USERNAME:PASSWORD@proxy.example.com:8080). | +------------------------------------------------------------------------+ 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. INSTALLING BIOPERL IN A PERSONAL MODULE AREA If you lack permission to install perl modules into the standard site_perl/ system area you can configure BioPerl to install itself anywhere you choose. Ideally this would be a personal perl directory or standard place where you plan to put all your 'local' or personal perl modules. Example: >perl Build.PL --install_base /home/users/dag >./Build test >./Build install This tells perl to install all the various parts of bioperl in the desired place, e.g. creating: /home/users/dag/lib/perl5/Bio/Perl.pm Then in your BioPerl script you would write: use lib "/home/users/dag/lib/perl5/"; use Bio::Perl; For more information on these sorts of custom installs see the documentation for Module::Build. If you are used to using something like: >perl Makefile.PL PREFIX=/home/users/dag You can get similar behaviour by using this instead: >perl Build.PL --prefix /home/users/dag For more information, see Module::Build::Cookbook documentation for Installing_in_the_same_location_as_ExtUtils::MakeMaker You can also use CPAN to install modules in your local directory. First enter the CPAN shell, then set the arguments for the commands "perl Makefile.PL" and "./Build install", like this: >perl -e shell -MCPAN cpan>o conf makepl_arg LIB=/home/users/dag/My_Local_Perl_Modules cpan>o conf mbuild_install_arg "--install_path lib=/home/users/dag/My_Local_Perl_Modules" cpan>o conf commit INSTALLING BIOPERL MODULES THE HARD WAY As a last resort, you can simply copy all files in Bio/ to any directory in which you have write privileges. This is generally NOT recommended since some modules may require special configuration (currently none do, but don't rely on this). You will need to set "use lib '/path/to/my/bioperl/modules';" in your perl scripts so that you can access these modules if they are not installed in the standard site_perl/ location. See above for an example. To get manpage documentation to work correctly you will have to configure man so that it looks in the proper directory. On most systems this will just involve adding an additional directory to your $MANPATH environment variable. The installation of the Compile directory can be similarly redirected, but execute the make commands from the Compile/SW directory. If all else fails and you are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the location of the modules (Bio/ in the distribution) since perl always checks the current working directory when looking for modules. USING MODULES NOT INSTALLED IN THE STANDARD LOCATION You can explicitly tell perl where to look for modules by using the Lib module which comes standard with perl. Example: #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; use Bio::Perl; #<...insert whizzy perl code here...> Or, you can set the environmental variable PERL5LIB: csh or tcsh: setenv PERL5LIB /home/users/dag/lib/perl5/ bash or sh: export PERL5LIB=/home/users/dag/lib/perl5/ THE TEST SYSTEM The BioPerl test system is located in the t/ directory and is automatically run whenever you execute the './Build test' command (having previously run 'Perl Build.PL'; if you have already installed BioPerl answer 'no' to script installation to get nicer test output later). For the 1.6 release and beyond, 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 ./ ensures you are using the Build script in the current directory to make sure you are testing the modules in this directory not ones installed elsewhere. The --test_files arguement 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 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. BUILDING THE OPTIONAL bioperl-ext PACKAGE The bioperl-ext package contains C code and XS extensions for various alignment and trace file modules (Bio::Tools::pSW for DNA Smith-Waterman, Bio::Tools::dpAlign for protein Smith-Waterman, Bio::SearchDist for EVD fitting of extreme value, Bio::SeqIO::staden). This Installation may work out-of-the box for most platforms except BSD and Solaris boxes. For other platforms skip this next paragraph. Of note, the code for bioperl-ext has not been updated along with the rest of bioperl, so one may expect to see some issues. If so, please report them to the BioPerl mailing list. Patches for these modules are always welcome. CONFIGURING for BSD and Solaris boxes You should add the line -fPIC to the CFLAGS line in Compile/SW/libs/makefile. This makes the compile generate position independent code, which is required for these architectures. In addition, on some Solaris boxes, the generated Makefile does not make the correct -fPIC/-fpic flags for the C compiler that is used. This requires manual editing of the generated Makefile to switch case. Try it out once, and if you get errors, try editing the -fpic line INSTALLATION Move to the directory bioperl-ext. This is available as a separate package released from ftp://bioperl.org/pub/bioperl/DIST. This is where the C code and XS extension for the bp_sw module is held and execute these commands: (possibly after making the change for BSD and Solaris, as detailed above) perl Makefile.PL # makes the system specific makefile make # builds all the libaries make test # runs a short test make install # installs the package correctly. This should install the compiled extension. The Bio::Tools::pSW module will work cleanly now.