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  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