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Bio
examples
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AUTHORS
BUGS
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FAQ
LICENSE
MANIFEST
MANIFEST.SKIP
Makefile.PL
PLATFORMS
README
biodatabases.pod
biodesign.pod
bioperl.lisp
bioperl.pod
bptutorial.pl

README

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: bioperl-l@bioperl.org

 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/
                     bioperl-bugs@bioperl.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...>