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This is the README file for the Bioperl central distribution, Version 0.9.0 *NOTE* This is a developer release for bioperl, the 0.9.x series does not guarantee a stable API between 0.9.x releases. These releases will be provided on a frequent (3-5 week) basis until the 1.0 release is prepared at the end of 2001. Please see the section on developer releases at the bottom. # $Id$ o Getting Started Thanks for downloading this distribution! For tutorials see Bioperl's bptutorial.pl or the online Bioperl tutorial at http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. For information on databases and Bioperl see biodatabases.pod. To look at example code browse the examples/ and scripts/ directories, and look at bioperl.pod for a descriptions of all these scripts. The bioperl.pod file also gives a overview of the history and purpose of Bioperl. For a discussion of issues in design and development please see biodesign.pod, recommended for those who want to contribute code. And for a list of OS's and versions that are known to support Bioperl see the PLATFORMS file. For info on installing Bioperl read on! o About Bioperl Bioperl is an association of developers of public domain Perl tools for computational molecular biology. Our website http://bioperl.org provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research. o Contact info Bioperl developers: email@example.com There's quite a variety of tools available in Bioperl, and more are added all the time. If the tool you're looking for isn't described in the documentation please write us, it could be undocumented or in process. Project website : http://bioperl.org Project FTP server: bioperl.org (anonymous FTP ok) Bug reports : http://bioperl.org/bioperl-bugs/ firstname.lastname@example.org Please send us bugs, in particular about documentation which you think is unclear or problems in installation. We are also very interested in functions which don't work the way you think they do! Please see the AUTHORS file for the complete list of bioperl developers and contributors. o System requirements - Not tested on anything but common forms of Unix (see the PLATFORMS file for more details) - perl 5.004 or later *. - ANSI C or Gnu C compiler for XS extensions - LWP (libwww-perl) modules for running network BLAST analyses (available from CPAN http://www.perl.com/CPAN/). - Additional perl module and application dependencies listed at http://bioperl.org/Core/external.shtml and in bptutorial.pl - Additional information using Bioperl with MacOS can be found at http://bioperl.org/Core/mac-bioperl.html - Additional information using Bioperl with OS X can be found at http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html * Note that most modules will work with earlier versions of Perl. The only ones that will not are Bio::SimpleAlign.pm and the Bio::Index::* modules. If you don't need these modules and you want to install bioperl using an earlier version of Perl, edit the "require 5.004;" line in Makefile.PL as necessary. o Documentation The "meta" documentation can be found in the bioperl.pod file. This should be the starting point for you to read about what bioperl is, how to use it and who wrote it. The bptutorial.pl file is a POD formatted tutorial document that contains useful information for new and existing Bioperl users. This file also contains a number of useful scripts that the student of Bioperl may want to examine. Use your favorite pod2* translator turn it into the format of choice or view it directly via perldoc. For example, go perldoc bioperl or in this directory go pod2text bioperl.pod | more pod2text bptutorial.pl | more pod2html, which comes with Perl, can be used to create web-browser navigable documentation files. Individual *.pm modules have their own embedded POD documentation as well. A complete set of hyperlinked POD, or module, documentation is available at http://www.bioperl.org. Remember 'perldoc' is your friend. You can use this to read any file containing POD formatted documentation without needing any type of translator. There is also an online course written at the Pasteur Institute. See: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. Useful documentation, in the form of example code, can also be found in the scripts/ and examples/ directories. The current collection includes scripts that run BLAST and retrieve full "Subject" sequences, make primers, retrieve ESTs based on tissue, align protein to nucleotide sequence, run GENSCAN on multiple sequences, and much more! See bioperl.pod for a complete listing. o Releases Bioperl releases are always available from the website http://www.bioperl.org or by FTP from ftp://bioperl.org. Each release is tested with the test suite and cross-tested on a number of different platforms. See the PLATFORMS file for more information on a specific platform. All efforts are made to release a bug-free package, however any known bugs in a release will be documented in the BUGS file. See the Changes file for a listing of what features have been added or what APIs have changed between releases. The 0.9.x developer series releases are intended to be quick releases off the main trunk to provided FTPable code that has been test that it will compile and all tests pass reasonably. In the future all odd numbered point releases will be developer releases and even point releases will be stable releases. o Install directions THE EASY WAY The Bioperl modules are distributed as a tar file in standard perl CPAN distribution form. This means that installation is very simple. Once you have unpacked the tar distribution there is a directory called bioperl-xx/, which is where this file is. Move into that directory (you may well be already in the right place!) and issue the following commands: perl Makefile.PL # makes a system-specific makefile make # makes the distribution make test # runs the test code make install # [may need root access for system install. # See below for how to get around this.] This should build, test and install the distribution cleanly on your system. This installs the main perl part of bioperl, which is the majority of the bioperl modules. There is one module (Bio::Tools::pSW) which needs a compiled extension. This needs an extra installation step. The directions for installing this are given below - it is almost as easy as installing the standard distribution, so don't worry! You may have some errors from the pod2man part of the installation, such as /usr/bin/pod2man: Unrecognized pod directive in paragraph 168 of Bio/Tools/Blast.pm: head3 You don't need to worry about them: they do not affect the documentation processing. To install you need write permission in the perl5/site_perl/ source area. Quite often this will require you (or someone else) becoming root, so you will want to talk to your systems manager if you don't have the necessary access. It is possible to install the package outside of the standard Perl5 location. See below for details. To install the Compiled extension for pSW you will need to read the next section of the manual. INSTALLING THE COMPILED EXTENSIONS This Installation works out-of-the box for all platforms except *BSD and Solaris boxes. For notes on this, read on. For other platforms, skip ahead to the next section, BUILDING THE COMPILED EXTENSIONS. INSTALLING 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 BUILDING THE COMPILED EXTENSIONS (OPTIONAL, ONLY FOR RUNNING LOCAL PROTEIN SMITH-WATERMAN ANALYSES FROM PERL) Move to the directory bioperl-ext. This is available as a separate package released from ftp://bioperl.org/pub/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 # Solaris/BSD users might need to edit the Makefile here 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. INSTALLING BIOPERL IN A PERSONAL OR PRIVATE 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. Note: you _must_ have write permission to this area. Simply pass a parameter to perl as it builds your system specific makefile. Example: perl Makefile.PL PREFIX=/home/dag/My_Local_Perl_Modules make make test make install This will cause perl to install the bioperl modules in: /home/dag/My_Perl_Modules/lib/perl5/site_perl/ And the bioperl man pages will go in: /home/dag/My_Perl_Modules/lib/perl5/man/ To specify a directory besides lib/perl5/site_perl, or if there are still permission problems, include an INSTALLSITELIB directive along with the PREFIX: perl Makefile.PL PREFIX=/home/dag/perl INSTALLSITELIB=/home/dag/perl/lib See below for how to use modules that are not installed in the standard Perl5 location. THE HARD WAY :) INSTALLING BIOPERL MODULES: LAST RESORT 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 below 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 or 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 PERL 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/My_Local_Perl_Modules/"; use Bio::Seq; <...insert whizzy perl code here...>