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README
This is the README file for the Bioperl central distribution,
version 0.7.2

# $Id$


o About Bioperl

  Thanks for downloading this distribution!

  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. 

  See the Changes and BUGS files for listings of what has changed
  since the last release and what known bugs are part of this release.

o Contact info

  Bioperl developers: bioperl-l@bioperl.org

  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
  - 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

  - Additional information using Bioperl with MacOS can be 
    found at http://bioperl.org/Core/mac-bioperl.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 rest of this
  file will tell you how to install bioperl)

  The bptutorial.pl file is a POD formatted tutorial document 
  that contains useful information for new and existing Bioperl users.

  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. 

  Remember 'perldoc' is your friend. You can use this to read any
  file containing POD formatted documentation without needing any type
  of translator.
 
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. 

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 effect 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...>
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