Ace.pm - Perl interface to ACEDB databases
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Ace
Freesubs
GFF
RPC
acebrowser
acelib
docs
examples
t
util
Ace.h
Ace.pm
ChangeLog
DISCLAIMER.txt
MANIFEST
Makefile.PL
README
README.ACEBROWSER
gff.txt
install.PLS
make_docs.PLS
typemap

README

This is version 1.86 of AcePerl, a Perl interface for the ACEDB
object-oriented database.  Designed specifically for use in genome
sequencing projects, ACEDB provides powerful modeling and management
services for biological and laboratory data.  For others, it is a good
open source introduction to the world of object-oriented databases

See the ChangeLog for important notices, including recent user
interfaces changes.  Please see DISCLAIMER.txt for disclaimers of
warranty.

INSTALLATION:

In addition to this package, you will need Perl 5.00503 or higher
(5.6.0 or higher recommended), and the Digest::MD5 module.  Both are
available on CPAN (http://www.cpan.org).

If you are using AcePerl to communicate with WormBase, a public server
is running on host aceserver.cshl.org, port 2005.  You can open a
connection to this server like this:

   $db = Ace->connect('sace://aceserver.cshl.org:2005');

Otherwise, if you wish to communicate with your own ACEDB database,
you must use ACEDB version 4.8a or higher, available from this
location:

	ftp://ncbi.nlm.nih.gov/repository/acedb/
	
To take full advantage of the sequence annotation features in the
Ace::Sequence and Ace::Sequence::Feature classes, you will need
version 4.9r or higher.

If you wish to use AcePerl in a client-server fashion, you must get
sgifaceserver up and running.  Some hints on installing the
sgifaceserver application are given later in this README.

Follow these steps to unpack, build and install AcePerl:

1. Unpack the AcePerl distribution with this command:

  gunzip -c AcePerl-X.XX.tar.gz | tar xvf -

  Replace X.XX with the current version number of AcePerl.

2. cd AcePerl-X.XX

3. perl Makefile.PL

   This script will ask you whether you wish to build: (1) the minimal package
   with support only for newer (socket) versions of the Ace server, (3) the maximum
   package, which supports both older (RPC) and newer (socket) versions of the 
   Ace server, or (2) a version that supports the socket server and has some C 
   language optimizations.  Choice (3) is recommended.  All versions will support
   local Acedb databases.

   The script will also ask you whether you wish to install support for the 
   AceBrowser Web server extensions.  Only answer yes if you are installing
   on a machine that already runs a web server and you wish to have AceBrowser
   installed.  If you answer in the affirmative, then you will be asked a number
   of directory configuration questions.  See README.ACEBROWSER for more details
   on installation.

   At this point, Makefile.PL will create the make files necessary to build
   AcePerl.  Among other things, the Makefile.PL script will attempt
   to guess the type of your machine and its operating system.  This information
   is needed to select the correct makefile in the ACEDB library
   directory, AcePerl-X.XX/ace/.

   If AcePerl fails to make correctly later in the process, it may be
   because the script guessed wrong.  You can override this guess by
   setting the machine type using the ACEDB_MACHINE environment
   variable.  On a C-shell or TC-shell machine, use a command like
   this one:
 
     setenv ACEDB_MACHINE ALPHA_4_GCC; perl Makefile.PL
  
   On a Bourne-shell or Korn-shell system, use:

    ACEDB_MACHINE=ALPHA_4_GCC; export ACEDB_MACHINE
    perl Makefile.PL

   You can find a list of machine definitions in
   AcePerl-X.XX/ace/wmake.  There are lots of them, but only
   one or two per operating system, so it's usually pretty
   easy to choose the right one.  The definitions have names 
   like ALPHA_4_GCC_DEF.  Before setting the corresponding
   environment variable, remove the "_DEF" from the end of the name.
   In case you're wondering the "4" stands for version 4 of the ACEDB
   server.

   Please drop me a line to let me know what you had to do to get
   the ACEDB libraries to compile.  I'll fix up the Makefile so
   that it works correctly for the next person who tries it.

4. make

   This will build the ACEDB client library, libaceperl.a, in the ace
   subdirectory.  It will then link in the Perl client subs.

5. make test (optional)

   You may "make test" to test the system.  It will attempt to open a
   connection to a database at beta.crbm.cnrs-mop.fr:20000100.  You may
   change these defaults by setting the environment variables ACEDB_HOST
   and ACEDB_PORT, or by defining them on the command line, as in:

    make test ACEDB_HOST=localhost ACEDB_PORT=200005

   However, since some of the tests are dependent on specific values in
   the database, this may cause some tests to fail.  Do not be alarmed if
   a handful of tests fail.  Do be alarmed if all of the tests fail.

  6. make install

  This will install AcePerl into your perl5 library directory.

  You may need to be root (superuser) in order to "make install".  This
  is because Perl will want to install the newly-built files into its
  library tree, /usr/local/lib/perl5/site_perl (or something similar),
  and this tree is usually not writable by mere mortals.  Do not
  despair: see the next section.

INSTALLING ACEPERL IN A NON-STANDARD LOCATION

By default, Perl will install AcePerl's library files within the
site-specific subdirectory of its library tree, usually
/usr/local/lib/perl5/site_perl.  If you wish, you can install the
library files elsewhere.

Simply change to the AcePerl distribution directory and run the
Makefile.PL script with the INSTALLSITELIB switch set to the full path 
of the directory you want to install into:

  perl Makefile.PL INSTALLSITELIB=/path/to/library

Then "make" and "make install" as described before.  You will now have
to tell Perl where to find AcePerl.  You can do this on a
script-by-script basis, or by defining an environment variable that
will affect all scripts.

To tell a single script where to find AcePerl, add a "use lib" line
to your script.  Put it _before_ the "use Ace" line:

  use lib /path/to/library;
  use Ace;

To change Perl's library search path so that it finds AcePerl
automatically, define the PERL5LIB environment variable in your
.login, .cshrc or .profile script.  PERL5LIB is a colon-delimited list 
of directories in which Perl will search for included libraries.  For
example:

  setenv PERL5LIB "/path/to/library";

If AcePerl was built as part of the main Ace distribution, you will
want to define PERL5LIB to be the location of the machine-specific 
build directory.  For example:

  setenv PERL5LIB $HOME/ace/bin.LINUX_4_OPT

Or you could reinstall AcePerl in the main Perl library tree just by
entering the wperl/ subdirectory, and rerunning "perl Makefile.PL"
without defining INSTALLSITELIB.

See ACEDB.HOWTO in the docs/ subdirectory for instructions on
obtaining and setting up the ACeDB database.  You'll find other hints
here too.

USING ACEPERL

A. Read the copious documentation
   
   perldoc Ace

B. Review the examples

A few useful examples can be found in the "examples" subdirectory.
Among these is a script called "ace.pl", which implements a text
interface to any local or remote ace database.  If you have the Perl
Term::readline module installed, it gives you command-line editing,
completion, and history.

The script "dump_cdna.pl" shows you how to dump out all spliced cDNAs
from wormbase.org.  Other dump scripts show similar tricks.  You can
use these as templates for doing other biologically interesting
tricks.

There is also family of CGI scripts that run on top of AcePerl to give
a WebAce-like interface to Ace (it is not as feature-full as WebAce,
but it is probably easier to set up and run).  This package is now part
of the AcePerl distribution, but is not installed unless you specifically
request it.  See README.ACEBROWSER for details.

INSTALLING THE ACEDB SERVER

See ACEDB.HOWTO in the docs/ directory for instructions on compiling
acedb and installing the server application to start up when needed.

Lincoln Stein
lstein@cshl.org