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This is the README file for the Bioperl central distribution,
version 0.05.1
# $Id: README,v 1.6.2.3 1999/06/25 13:37:15 birney Exp $
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://bio.perl.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: vsns-bcd-perl-guts@lists.uni-bielefeld.de
Project website : http://bio.perl.org
Project FTP server: bio.perl.org (anonymous FTP ok)
Bug reports : http://bio.perl.org/bioperl-bugs/
bioperl-bugs@bio.perl.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!
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/).
* 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)
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
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 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
Move to the directory Compile/SW. 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 TO USE Readseq
Edit the top of Bio::Parse.pm to show the path to readseq, ie
edit
## Uncomment the $OK stuff (it is mentioned twice to
## shut strict up. Set $READSEQ_PATH to the full path
## to the readseq executable.
## $OK = "Y";
## $OK = "Y";
my $READSEQ_PATH=undef;
to something like
## Uncomment the $OK stuff (it is mentioned twice to
## shut strict up. Set $READSEQ_PATH to the full path
## to the readseq executable.
$OK = "Y";
$OK = "Y";
my $READSEQ_PATH='/usr/local/bin/readseq';
The use of readseq like this has been officially 'deprecated', waiting
for a better system in 0.06 which will be much more transparent as
to what is going on.
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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